


No Refuge

by Liathwen



Category: Sherlock (TV), Star Trek: Alternate Original Series (Movies)
Genre: Dubious Consent, Explicit Language, F/M, Mildly Dubious Consent, Violence, khanolly
Language: English
Status: In-Progress
Published: 2014-04-05
Updated: 2015-07-12
Packaged: 2018-01-18 06:00:23
Rating: Explicit
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 19
Words: 26,126
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/1417772
Author URL: https://archiveofourown.org/users/Liathwen/pseuds/Liathwen
Summary: <blockquote class="userstuff">
              <p>Khan manages to salvage three members of his crew and awakens them. One of them, Molly Hooper, remembers snippets of a past life. A past that Khan has no knowledge of.</p>
            </blockquote>





	1. Khan

**Author's Note:**

> Well, apparently I'm a masochist because I've started this fic while I still have 3 to finish. Bear with me. Blame Miz-Joely who posted a bunch of Khan!lock stuff on Tumblr and got the gears of my brains turning. It's all her fault.
> 
> Anyway this one will be a wild ride, with some violence, some dubcon and lots of language so you are warned.
> 
> Our story begins with the scene in Star Trek Into Darkness where Khan is demanding that his crew be beamed aboard his warship and goes au from there. I hope you enjoy!

Khan scanned the torpedoes for signs of life.

_Damn, they’re almost done removing the capsules, Marcus’ daughter is cleverer than I gave her credit for._

Khan Noonien Singh growled his discontent lowly, softly enough that the sound did not transmit through to the other ship through the open communication link. His vibrant blue-green eyes flashed with annoyance that his plan had gone awry and he was unable to take the full number of his sleeping crew from the depths of the Spaceship _Enterprise_.

There were seventy-two in all. Seventy-two faces, seventy-two of his brethren locked in capsules, deep in cryosleep. He’d placed them there, in the torpedoes. He had wanted to keep them safe. When he thought that his crew had been taken from him, murdered in their sleep, he’d gone after his suspect with a vengeance. He wasn’t sure why his fury had consumed him as completely as it did, he was only aware of a deep, aching sense of loss that he couldn’t understand.

Khan’s brow furrowed in annoyance. His brilliant mind could see all of their faces, however, he did not actually remember any of them. Their personalities were lost to him, a fact which he chalked up to an effect of the cryosleep.

_I will remember soon,_ he told himself, just as he had every day for the nearly eleven years since he’d been awoken from his age-long slumber.

Khan’s sculpted torso rippled under his fitted black shirt, the uniform of the hated Starfleet of which he had been a part under the pseudonym John Harrison, after he was awoken by the greedy and ruthless Admiral Marcus. His long, musician’s fingers tapped the arm of his chair, the captain’s chair of the warship _Vengeance,_ ( _aptly named_ , he thought,) biding his time, waiting for the analysis of his targets to be complete.

He was perfect, a feat of genetic engineering. Khan was stronger, faster and smarter than the puny humans in the ship in front of him. He was superhuman in all aspects.

His body was a machine; he’d proven it again and again, not the least of times being when he single-handedly destroyed the group of attacking Klingons to save the crew of the _Enterprise._ Not that he cared if they lived or died, but he’d deduced by that time that the missiles they were threatening him with held the bodies of his crew so it was necessary to save them in order to surrender to them.

He was incredibly fast, obliterating his enemies in seconds with his incredible strength. No mere human could best him, and even the Klingons had fallen before his fury like wheat before the scythe.

But as superb as his body was, it was only transport for the most important aspect of his existence, his brilliant mind.

He had mastered the art of controlling his mind, filing away all the useful data in a secure location. Khan pictured a dwelling, small but comfortable, with each room holding a different set of information. He didn’t know why the wallpaper of his mind palace, as he called it, had the startlingly graphic black and white pattern, or why there was always a skull on the mantelpiece. Khan wasn’t even sure why one of the doors opened to reveal a pristine, white morgue. He just knew that when he closed his eyes and walked through his mind, that was what he saw. So that is where he stored the information he needed to remember. His system worked quite well and he was able to call up data that others would have long forgotten.

He narrowed his cat-like eyes at the screen, while checking out of the corner of his eye if he could lock on to the remaining three capsules that carried his crew without arousing suspicious.

He could.

His hand slid out, slowly, and he pressed the cool button, smirking as he did so. Within seconds, there was shouting on the screen in front of him and he grinned coldly, triumphantly, running a hand through his dark hair, as the capsules materialized in the room with him.

“Well, Mr. Spock, I do believe that our business is concluded for today.” Khan spoke to the image before him, his voice both taunting and cruel. He would not let them see that he was in the least irritated he’d only managed to save three members of his crew from them, though he was sure that the ones left behind would be safe enough. They would not be slaughtered in their sleep now that Marcus lay dead.

“We still have the vast majority of your crew,” came the answer, spoken by the ever logical Vulcan. Khan respected him, as his intelligence was far above that of the captain of the _Enterprise_ , Kirk, who was all brawn and very little brain. While Khan did use his superhuman body to his advantage, it was his cutting brilliance that really set him a step above the rest of humanity and he knew it.

“Do not mistake me,” he snarled, condescendingly, “I said for today. I will be back to collect the rest of my crew and lay waste to yours.”

With that threat, ( _promise,_ he told himself,) he flipped the switch he had prepared beforehand and his ship disappeared into deep space, carrying himself and his three sleeping crew members.


	2. Familiar Faces

**Notes for the Chapter:**

> Thanks for all the encouragement!

Molly Hooper woke slowly, blinking in the bright sunshine that streamed in the window.

When she could focus, she looked around. The room she was in was drab, the walls and floor a dull, lifeless, grey with the only sign of color being a vase of gorgeous flowers on her bedside table. The cheerful scarlet and yellow hues lighting up her face with a brilliant smile.

Her bed was placed against the wall opposite the main door which was actually a huge window, the glass taking up the entire area where a wall should have been. She looked outside, her eyes narrowing at the view. It was barren and rocky, and Molly couldn’t think of a single place on Earth that looked like that, though, for some reason, it was achingly familiar.

She turned back to the room. Another door, which she assumed was the bath, was on her left. Molly made to move, groaning loudly as her whole body protested. She felt like she’d been hit by a truck. All her muscles were sore and she groaned again.

The door opened and a man entered. He looked vaguely familiar, but Molly couldn’t place him.

The man was relatively short, not much taller than she was, Molly guessed, and had sandy blonde hair, cropped in the military fashion. His posture was rigid, ingrained in him, giving her further evidence of a military background. His eyes were a grey blue, like fog or the sea after a storm. There was something honest and right about him, which gave Molly a sense of security to calm her uneasiness.

He smiled at her, a genuine one that lit up his face, and spoke.

“How are we feeling, Doctor Hooper?” he asked, holding up a black medical bag, a silent request for permission. Molly assented.

“I’m not really sure. I’m very confused,” she replied as he moved over to her and set his bag down, rummaging through it for a stethoscope and light. He listened to her heartbeat as he answered.

“Well that’s perfectly normal. Cryosleep tends to make people forget things, though it affects some people more than others.” He was all business, pointing to the light to indicate Molly should follow it with her eyes, which she did.

“Cryosleep?” she interrupted, part of her not understanding, while the other part seemed to have a scientific knowledge of the subject. _That’s strange._

He raised a brow at her.

“Right, cryosleep,” she amended, lamely.

He smiled again. “Do you remember me?” he inquired, a curious expression on his face. She nodded but her brow furrowed.

“You seem familiar somehow but I don’t know your name or where I know you from,” she gave him an apologetic look.

“Don’t worry about it, it’s exactly the same for me. I recognize you but I have no idea why. I suppose we were crew mates, and since we are both doctors, we probably worked together. Maybe the amnesia will wear off and we’ll actually remember,” he paused, frowning. “But for now,” he held out his hand to Molly, “I’ll introduce myself. I’m John Watson.”

The small woman took his hand and introduced herself as well, though it wasn’t strictly necessary considering he’d known her name already.

“Molly Hooper, pleased to meet you.”

He grinned at her. “Well Molly, you appear to be in perfect health, no adverse effects from the extended cryosleep. That’s very good. If you feel nauseous, the loo is just there,” he pointed to the door on the left.

“How long were we asleep?” she asked, curious.

The doctor’s brow furrowed. “You know, I have no idea. You’ll have to ask him.” He gathered up his bag and made for the door.

“Ask who?” Molly questioned, highly confused.

He gave her an odd look, before saying, “Oh he’ll be along in a little while, I’d bet. He showed up not long after I woke up.”

She glanced at him startled, wondering what she had missed. “How long have you been awake?”

“Oh, just a couple days. You took the longest to come out of it. In fact, I think he was a little worried.” John stared down at the floor guiltily, as if he was giving away an enormous secret.

“Who?” she asked again. “Who was worried?”

“He’ll be along,” he repeated his words from before. “I’ve got to run. Rest. I’ll see you in a while.” With that, he left, closing the door softly behind him.  

_What happened to us?_

Molly stood shakily and made her way slowly to the bath, relieving herself before washing her hands and staring at her reflection in the mirror for a few minutes.

She was pale, but not overly so, considering she’d spent who knows how long in a tube. Her large chocolate colored eyes stared back at her from a plain face, with a smattering of light freckles here and there. Her nose was small and upturned, and her mouth was quite the same. Her thin lips, _nothing pouty about that mouth_ , were a dark pink. Her brownish-red hair was down, flowing around her shoulders, and she crinkled her brow. _That’s not right._

She fumbled through the drawers, finding a hair tie, then a toothbrush and toothpaste and proceeded to clean her teeth before deftly pulling her hair into one long plait down her back. She nodded at the mirror in satisfaction. After completing her self-appointed tasks, Molly made her way back to her bed slowly, exhaustion making itself evident in her heavy limbs.

Collapsing onto the bed, she tried to remember something, anything, but everything was a blank before she fell asleep. Her brow winkled in concentration but the only things she could remember clearly seemed more like someone else’s memories. Like she’d seen a movie and the plot had replaced her own past. It was strange. Frustrated, she sat up, dangling her legs off the bed, her hands clasped in her lap.

She specifically remembered working as a doctor aboard a spaceship. She remembered her crewmates, and seeing all kinds of different planets. The problem was that she kept getting the distinct feeling that what she remembered wasn’t what it was supposed to be.

The petite woman stared, unseeing, at her hands, her brow crinkled in thought. She couldn’t piece together anything certain, but there were flashes of another life. One that felt more, well, **_right_**. A cold white room, a black and white cat, dark curly hair, and a cherry print jumper.

She didn’t understand why she had these competing pasts. It was driving her spare.

She was deep in concentration, and so didn’t hear the door open, or see the tall figure step inside and stop dead, studying her.

After a moment, Molly caught some movement out of the corner of her eye and looked up, startled.

Standing just inside the door, watching her intently and with some emotion she couldn’t quite name, was the most beautiful man she had ever seen. His intriguing eyes captured Molly’s attention and her breath hitched. She stared at him for a minute, with him studying her just as closely. Her eyes narrowed; something was off about him, something didn’t look right. Suddenly it dawned on her. She recognized this man.

“Sherlock!” she cried happily. “Wait, what happened to your hair?”

His brow furrowed as he gazed at her silently.

“My name is Khan,” he replied, ignoring her question, his eyes flitting over her body. “And you won’t forget that, will you, Molly Hooper?”


	3. First Contact

**Notes for the Chapter:**

> Special thanks to Miz-Joely and Lisape for letting me throw random ideas at them and vent when nothing worked.

Khan moved like a big cat. Full of grace and agility, but power was evident in every movement, his muscles rippling beneath the dark material of his fitted black uniform. He advanced swiftly until he was at Molly’s bedside, looking down at her. Her breath caught as he slowly, deliberately bent down, forcing her back against the bed.

Molly stared wide eyed at the man who was now leaning over her, heart beating fast at the sight of Sherlock ( _Khan,_ she reminded herself, _why do I keep thinking of him as Sherlock_?) so close to her.

\-----------------------------

Khan smirked down at the small woman beneath him. She was exhibiting clear signs of arousal; face flushed, pupils dilated so wide that only a tiny ring of the chocolate colored iris still showed.

He couldn’t explain what it was that drew him to her. She wasn’t beautiful by most standards. True, she was alluring in her own way, but if he were to describe his thoughts on beauty, it wouldn’t be her picture painted by his words. No, it wasn’t beauty that drew him to her. And while, yes, she was highly intelligent if her files were anything to go by, she wasn’t anywhere close to his own level. Khan had spent many hours since he’d initiated her awakening from the cryosleep pacing and trying to sort out the intense desire he felt for her. He hadn’t made any progress.

He’d devoured ever bit of information he’d been able to find on her in the three days since he’d begun the process of waking her. The two men had come out of the sleep easily and Khan had found himself very worried when she took longer. He told himself he was as concerned for every member of his crew, but that just wasn’t the truth. The little woman wormed herself into his thoughts far too often for not even being awake.

Khan didn’t even know what she was like yet.

He painted a picture of her in his head. He thought she’d be a little shy, a little awkward. _Prone to make morbid jokes_ , he decided when he saw her specialty in pathology. _Likes color_ , when he saw the photo attached to her file. She looked like a cat person as well. He had shaken his head vigorously after that, attempting to dislodge his wandering thoughts. He took to sitting in her room on the second day, watching her deep breaths, waiting for her to wake up.

He was there when she began her first movements, signaling that she was finally coming out of the deep sleep. He’d rapidly exited her quarters and gone to find the other doctor, John Watson, and told him to be ready to give her a check over when she was fully awake. He’d gone back to his own quarters after that and paced back and forth. His nerves were getting to him and his brow furrowed.

Now, staring down at her, inhaling her sweet scent, lemon and strawberry shampoo, (he made a mental note to find some exactly like it for her,) and milk and honey from the hand soap she’d used, Khan was more confused than ever.

He wanted her, badly. He wanted to press her back into her bed, take out his cock and brand her as his. So everyone would know that she belonged to him. His eyes narrowed as his thoughts ran away with him and he felt the first tremors of his body indicating arousal. He pulled back suddenly, leaving her staring at him wide-eyed and breathing heavier than before. He smirked, some primal part of him satisfied that he had that effect on her without even touching her.

He held out his hand silently, pulling a syringe out of his pocket, and waited for her to give him her arm. He had to test her blood, to see if she was augmented. It had been a shock to discover that only one of the other two of his crew had been given the drug that Khan had flowing through his veins. The doctor was quite normal, not exhibiting any of the superhuman traits Khan possessed. After a few simple tests, it was determined that he had never received the injection.

The other man, one Gregory Lestrade, was an augment, though his skills still weren’t up to the level that Khan’s were. He’d felt a smug sense of pride, knowing that even with the enhancement to his body, that Khan was still better than everyone, even his augment brothers.

As he took the blood from her silently proffered arm, Khan thought about whether her being an augment or not would affect his desire for her. When she gasped a little as he removed her needle and bit her soft lower lip, he knew it wouldn’t matter one bit whether she was human or an augment. She was already far from normal.

“Report to the bridge in an hour,” he ordered, his eyes noting the time on the old-fashioned clock on her table next to the flowers he’d put there. It’d taken a completely unnecessary trip to a populated planet to get them, but he didn’t think twice about it for some reason. There were no flowers on this planet where he’d landed the ship. It didn’t matter, this was just a stop along the way. A layover, if you will, to regroup and assess the situation.

He would make sure the planet they finally settled on had lots of flowers.

His brow furrowed in confusion and he turned without another word, leaving the room and making his way through the halls to the lab. He stopped in on Lestrade and Watson on the way, delivering the same order to them.

\-----------------------------------

Molly sat perfectly still long after he left, thoughts and heart racing.

He was undoubtedly the most handsome mad she’d ever seen. He was fascinating, from his ever-changing light eyes and strong build to the confidence he exuded with every movement. She chewed her lip. She’d had such a visceral reaction to him, half hoping when he leaned over her that he would snog her silly. Molly blushed as she remembered the intense look on his face as he approached her. She could imagine that look as he explored her body, teasing and possessing her.

She stayed lost in her thoughts for a good while, before jumping up a little too quickly, realizing that she didn’t have much time until she was supposed to go. She swayed a bit, but managed to keep to her feet, before heading out of her room to find the bridge.

\---------------------------------

When he arrived at the lab, he found he had to take a deep breath to be able to concentrate on the tests. His mind was filled with images of the petite woman. Her smile haunted him.

It was then that he remembered that he hadn’t actually seen her smile yet. The image that his mind conjured up was so real though, it was almost like a memory.

_A memory._

He shook his head. No, it couldn’t possibly be a mere slip of a woman that caused his memories to return. That smacked terribly of sentiment and Khan knew that was one of the very few areas he was severely lacking in.

She tested negative for the components that made up the blood of an augment. She was completely, totally human. Khan sat for a few minutes more, wondering how, if she was ordinary, she could capture his attention so fully. He shook off his thoughts, checking the time, and headed up to the bridge to address his small crew and discuss where they went from here.


	4. Human Life

**Notes for the Chapter:**

> Another chapter, and so quickly too! Enjoy!
> 
> Thanks Miz-Joely for reading over and correcting for me!

Molly arrived at the bridge and said hello to John, who inquired how she was feeling, to which she replied that her muscles were a bit sore but she was otherwise fine. He smiled at her, assuring her that he had felt the same when he woke up, and introduced her to the other man in the room.

“Molly, this is Gregory Lestrade. Greg, Molly Hooper. She’s medical too,” John said, by way of classifying her.

“Doctor Hooper?” the silver-haired man clarified, and Molly nodded shyly.

“It’s a pleasure to meet you,” he said, ducking down to kiss the back of her hand just as Khan entered the room.

\-------------------------------

The now captain of the _Vengeance_ scowled as Molly blushed at the older man’s gesture and cleared his throat loudly, making the petite woman jump and look over at his in surprise.

“I believe introductions are over. Down to business.” He stalked further into the room, going to a computer screen and rapidly typing in a series of passwords.

“As of four days ago, we all are wanted by Starfleet for crimes against humanity.”

Molly’s eyes went wide, fear in them, but she remained silent. The two men reacted less, having already been told part of the story soon after they woke from the cryosleep.

He searched through the Starfleet archives and clicked on the video of himself in the wreckage of the Starfleet building in London. He flipped to the files on himself as John Harrison and the file concerning Admiral Marcus’ plan to use Khan to build weaponry for the war he wanted with the Klingons.

Khan’s eyes kept darting to Molly, who grew more and more pale as she silently read the documents and listened to him tell his version of the story. For his part, he grew frustrated, wondering why she wasn’t sympathizing with his reasoning. All he’d wanted to get his crew back. The only reason he’d attacked Starfleet in the first place was to exact his revenge on Marcus for the supposed death of his family.

“At first, I believed that we were all augments; humans, giving a serum which enhances strength and agility, along with whatever intelligence that was possessed originally. However, it has come to light that we were not all dosed with the drug. Lestrade,” he nodded at the man, “and I are. John, and you, Molly, are not. I don’t know the reason for that but I intend to find out.”

When he was finished with his explanation, Khan launched into his ideas for what to do now.

“Obviously, we won’t be safe on any planet that Starfleet has access to. Fortunately, there are still many planets that they don’t bother with, so we should be able to find something suitable for us when the need arises. First things first though, we need to infiltrate the area the rest of the crew is being held in and get them out.”

He sighed. Only he and Lestrade were augments, which meant Watson and Molly were at a serious disadvantage, being no stronger than those guarding the other sleeping members of their crew.

“We’ll have to figure out where they are being held before we can plan anything further, which means someone will have to go undercover into a Starfleet controlled area. We’ll discuss it more when we’re closer to putting our plans into action. For now, I have more research to do to fully prepare us for whatever situation might arise.”

He stood, the others falling back a step or two, and turned to face them.

“We are fugitives and will be detained on sight if we are recognized. In my case, they’ll probably forgo the detainment and simply attempt to kill me. That being said, there is no mercy for them.” His voice was icy. “Do not hesitate to kill them if you need to.”

\-----------------------------

Molly couldn’t stand it any more. This beautiful, fascinating man was in fact, cruel and cold, and she was heartbroken. Before she realized what she was doing, she opened her mouth to berate him.

“They’re just people, Khan! They’re only doing what they are told to do. They’ve done nothing to us, why are you so cruel?!”

The expression on his face was pure confusion.

“Molly, they have the rest of us held captive. Everything I did, everything I am prepared to do is to keep my crew safe.”

“But they haven’t done anything to them!” Molly cried out. “They’re safe! If we can work out a way to get to them without bloodshed -”

Khan cut her off. “You have to be prepared to do anything, Doctor Hooper,” he said, steel in his voice.

“I’m not prepared to kill an innocent person,” she replied quietly, but with a determined set to her jaw.

\-------------------------

He stared at her for a moment, honestly surprised that she had the spine to stand up to him. He knew he was intimidating and to such a small women even more so. But here she was, berating him for caring more about his own crew than about the lives of the miserable Starfleet minions.

He would **_make_** her see his point of view. He thought briefly before a malicious smile spread over his face. He’d shame her into it.

“Then what good are you?”

Molly stared at him in shock for a moment before doing the exact opposite of what he expected. She stared him straight in the eyes and smirked.

“None, I suppose.”

With that bit of defiance, she turned and fled the bridge, John and Lestrade looking first at Khan, then following her, calling Molly’s name as they went.

\----------------------------

Molly swallowed down the tears that threatened as she ran out of the room, needing to put distance between the cold man who held her attention so firmly. His rage and callous disregard for others sickened her, but try as she might, she couldn’t hate him.

Anything that might have been between them was out of the question now though. No matter how attracted she was to him, Molly wouldn’t allow herself to act on it. Not when he could treat people as if they were disposable, their lives meaningless. She found herself in the medical bay, and sighed in relief at the familiarity of her surroundings. All Starfleet ships were outfitted with similar equipment and she ran her fingers over the microscope near her. There were signs that it had been used recently and she noticed a syringe in the nearby hazardous waste bin.

Khan had been here analyzing her blood.

The thought made Molly despair again. She was only human, what could she do in the face of his overwhelming strength of both body and mind. She crumpled to the floor, burying her head in her hands as the shouts of John and Lestrade came closer.

The men entered the room, both approaching her and kneeling down next to her.

“It’s ok, Molly. It’ll be alright,” Lestrade soothed.

\-----------------------------

Khan didn’t go further into the medical bay than the doorway. His light eyes flicked over the small woman, noting in annoyance that Lestrade was touching her again. John noticed his presence almost immediately and stood, making his way over to where Khan was, casually leaning on the wall next to him.

“You know that’s a bit not good,” the doctor said, his eyes also on Molly and Lestrade.

Khan glanced at him, his eyes flashing with curiosity. “Why does it matter? I did it all to get you, my crew, my family, back. Even if I can’t remember any of you,” he added bitterly.

“I know. And I might have done the same, I don’t know. But she’s good.” John looked up at Khan, who was still watching the tiny woman talk to the other man. “She’s innocent. And she can’t understand why sometimes bad things have to happen for the good of others.”

Khan gulped and nodded, deciding that he liked the man next to him. They stood for a moment in silence, the man’s presence soothing Khan’s jealousy and anger for some reason he couldn’t name. Finally, John pushed away from the wall he’d been leaning on and turned, inclining his head to Khan.

“Well, I’ll be off, with your permission. I’m still feeling some of the effects of the cryosleep,” he said, rubbing his shoulder absently.

Khan nodded, allowing a brief quirk up of his lips at the doctor’s retreating back, before turning his attention back to the pair on the other side of the room. His eyes narrowed as Greg patted Molly on the shoulder then drew her in for a hug. His fists clenched as Molly sobbed into the other man’s shoulder.

Right then, Khan made up his mind.

_MINE._

He wanted Molly Hooper, more than he could ever remember wanting someone. He didn’t bother trying to fool himself, he knew he was incapable of sentiment, of love, but desire was an impulse he was well acquainted with. He needed her in his bed, moaning underneath him as he moved within her. He wanted to tie her to the bed and fuck her until she screamed his name over and over. He intended for the whole ship to know that she was his and to hear his name frantically yelled by his little woman in the heat of passion as he filled her wet cunt with his cum.

Khan eyed Molly, deducing her body language.

She would not go willingly, not at first. Not now that she knew what he had done. No, she’d be difficult about it and he had no desire to force her. When he took Molly, he wanted her to be happy about it. He wanted her pliant and willing, begging to serve his every need. He wouldn’t force her, but he wouldn’t stop pursuing her.

He steepled his fingers, rubbing slightly on his full lower lip as he pondered the conundrum. His eyes lit up and lips quirked ever so slightly as he hit on the solution to his problem. He nodded to himself. A slow game of seduction then. He’d make her crave him. Crave his voice, his touch, his presence. Make her desire him as much as he coveted her. She wouldn’t realize what was happening until it was too late to turn back.

 _Then_ , he assured himself, _then she’ll be mine._


	5. Strategies

**Notes for the Chapter:**

> Sorry about the long wait for this chapter... the story is about to pick up the pace. Hope you enjoy!

“Doctor Hooper.”

Khan’s low baritone rumbled through the Medical Bay, echoing slightly against the metal of the tables and coolness of the sleek cabinets and floors. Molly jumped, a frightened yelp escaping her in her surprise at his presence. Khan had entered in near silence and had been watching her for several minutes.

She’d been at a microscope examining a sample of Lestrade’s blood that she’d finally worked up the courage to ask for a few hours earlier. The silver-haired man had smiled and acquiesced, gently chastising her for waiting so long to ask for it when it was obvious she was incredibly eager to get her hands on it. She’d blushed, unaware that Khan had been standing in the hall just beyond the door of the room they were in and had clenched his hands into fists, upset that she was more comfortable asking Lestrade for something as intimate as his blood than she was asking him for anything, even basics.

In fact, that she was speaking to Lestrade at all, when she’d shied away every time Khan entered the room she was in. She’d make some excuse and scurry away, but not before his keen eyes detected the hint of a blush trailing from her cheeks down to stain her neck. He desperately wanted to know how far the flush went down her slim frame and had to keep a tight leash on his urges. If he didn’t, Khan knew he’d take her, permission or not, and everything would be ruined.

Now though, she was alone in the medical bay, seated in front of her microscope, with a tablet next to her, on which she was jotting quick notes in her loopy handwriting. Most of the room was shrouded in darkness, save for the small area she occupied and the atmosphere was calm.

Khan stalked into the room and opened a cabinet, rummaging around for supplies, then turned to the fridge, pulling out a vial of his own blood and setting everything down in front of the microscope next to Molly.

The petite woman had gone back to her examination, studiously ignoring the male sauntering about the room, but Khan could see that ever present blush beginning to form and creep its way down her neck. He smirked and settled next to her, preparing a slide. He’d been examining his own blood, fascinated by the regenerative abilities he possessed and was subjecting the sample to various traumas in order to ascertain just how much damage he could withstand. They worked in silence for about half an hour before he decided to speak.

“Molly,” his tongue caressed her name as he looked up from his microscope.

She jumped slightly, and he smiled to himself. She’d gotten so lost in her work that she’d almost forgotten he was there and had relaxed considerably. He’d been watching her out of the corner of his eye and couldn’t help thinking that she was most beautiful when given something to study.

“Could you get me some more slides?” he asked, more in the tone of an order than a request. He was curious as to how she would react to his eliciting her help in small ways and was gratified when she immediately hopped up with a small “of course,” and fetched several clean slides for his use.

_She needs a white lab coat. She’s not complete._

Khan’s brow furrowed as he watched her move around the lab. He couldn’t pinpoint why, but he couldn’t get the idea of her in a lab coat out of his mind’s eye. It wasn’t a sexual fantasy either; not that that wasn’t appealing, but it was something else. It seemed right for some reason. He frowned, searching his mind, but came up with nothing concrete, just the image of her in the coat. He smoothed his features as she returned with the slides.

Khan took them from the little woman before she could set them down and brushed his fingers along hers, ignoring the shock that the feel of her skin sent through his system, focusing on her face instead. Her eyes widened ever so slightly and she pulled her hands back quickly. He fought the urge to smirk and kept his expression neutral.

She didn’t sit back down and instead gathered up the materials she was using and cleaned up her space quickly, before murmuring that she’d finished and intended to retire to her quarters. He nodded, frowning slightly.

Molly left the lab and Khan sat back, running a hand through his hair. It felt right being there with her, working quietly side by side. He let out a growl of frustration and left his things were they were, before stalking out of the medical wing and to the captain’s quarters.

\---------------------------

Five hours later, Watson poked his head in Molly’s door after knocking, and found her reading on her tablet.

“Hey Molly, he wants us to see him. Apparently he’s found something. Sounded impatient.”

John frowned, and Molly scrambled up, adjusting her clothes, fitted black trousers with a matching black long sleeve shirt and black knee high boots. She’d planned on staying in her room for the rest of the night, and so hadn’t been bothered that her outfit matched Khan’s but now she was regretting her choice. Not that there was much to choose from but surely she could’ve found something else. Changing was out of the question though with Doctor Watson waiting for her at the door. She sighed and joined him, walking swiftly towards their destination.

Khan was standing just inside the room, which looked to be some sort of conference or planning room. It was relatively small, just large enough to house a table surrounded by chairs. He motioned to them and Molly took a seat next to John and across from Lestrade. Khan stood between Lestrade and Molly leaning, supported by his hands, at the head of the table and issued a verbal command to the screen at the other end of the table. It lit up with a map, showing the greater London area.

Molly’s eyes widened as she looked at the map, reading street names, barely hearing Khan’s words as he spoke about Starfleet headquarters. She recognized many of the names and opened her mouth to speak before she thought.

“Are we from London?” she asked, interrupting Khan in mid-sentence. The three men stared at her and Khan narrowed his eyes, examining her face. Instead of annoyance, after a second of scrutiny, she saw a spark of excitement light up his eyes.

“You are familiar with this map?” he questioned and his face broke out into a pleased expression when she confirmed his assessment of her.

“I do, some of the street names are very familiar,” she answered, looking again at the map.

“John, Lestrade?” Khan inquired, but received negative responses from them.

“I didn’t recognize it the first time I saw it either. It seems that Doctor Hooper has more of her memory than the rest of us.”

Molly glanced down at the table quickly, thoughts of her competing memories floating through her head. Her brow crinkled and she missed the analytical gaze of Khan turned on her before he continued with his briefing, pointing out key buildings and other sites.

“I’ve pinpointed these two areas as the most likely places for them to be holding the rest of the crew. How we’ll get them out is another matter. I can’t be seen, or at least I can’t be recognized by anyone and I surely would if I strutted into a Starfleet facility. They don’t know your faces though so there’s our advantage.”

Molly looked up sharply. “I’ll go.”

All three of the men protested, Khan most vehemently.

“No Molly,” he commanded, his voice strained. “If you are recognized-”

“You just said they don’t know what we look like,” she answered, excitement and resolve building within her. “And besides, I’m the only one who remembers anything. Perhaps if I see something familiar, it’ll help.”

There was silence in the room until Lestrade spoke up.

“I could go with her.”

\--------------------------

Khan’s head shot up from where he had been glaring daggers at the tabletop.

“No,” he ground out, barely controlling his anger at the thought of Lestrade going with Molly into the city, leaving Khan to wonder what they were doing, what he was saying to her.

“It makes sense,” John said slowly, his eyes flitting back and forth between Lestrade and Molly before landing on Khan. “I’m not an augment, I wouldn’t be able to protect her very well. Lestrade could keep her safe and she could lead him through the city. It’s ideal.”

 _Ideal? No, the situation is far from ideal._ He glanced back at the petite woman next to him, and sighed inwardly. Her jaw was set and her eyes gleamed. He admired her, the determination in her form was almost palpable. She would not fail in her mission, not if it could be helped.

He wasn’t happy about it, but sending Lestrade with her would be safest, and he found himself very unwilling to risk any hurt to her, whether it meant letting her go with his apparent rival or not.

Not that Molly knew of the other man’s affection for her. He hadn’t been as overt about his attraction as Khan had. The captain’s chest swelled unconsciously as the thought crossed his mind that Molly hadn’t given Lestrade the looks that she’d thrown in his direction when she thought he wouldn’t notice. Her delectable blush was missing around the older man as well.

All in all, Khan was fairly confident that she was not interested in Lestrade. It eased his worry slightly.

“Fine. We’ll begin tomorrow,” he snapped, and sat in his chair. They needed to talk strategy and he wasn’t going to leave anything to change with Molly in the line of fire.


	6. Infiltration

Molly tried to still the rapid pounding of her heart as she ran through the alley trying to call up the image of the map in her head. Her breath came in ragged pants, and she skidded to a halt at an intersection, glancing frantically both ways before taking off down the sidewalk, dodging people and shouting her apologizes when she managed to bump into someone.

She could hear her pursuer gaining on her, and she mentally cursed her lungs as they screamed out for oxygen.

Molly turned abruptly, ducking into a dark alley, hoping whoever was chasing her would pass by. She breathed a sigh of relief when they did and turned to walk out the other side of the passage, but froze when a tall figure stepped from the shadows in front of her. It wasn’t the person who had been following her, but it wasn’t a person she recognized either. Molly opened her mouth to scream just as his hand landed on her mouth smothering her attempt to attract attention.

“I’m so sorry, Miss Hooper,” said a calm voice as Molly registered the feel of a body behind her and a syringe in her upper arm. She squirmed helplessly as he pulled the small metal object from its place clipped to the inside of her collar and dropped it to the ground, smashing it underfoot. Shortly after there was a tingling in her body and her eyes drifted closed as her body went limp and she slumped to the ground.

“Alright let’s get her to the base before he locates us and all hell breaks loose.”

“Yes sir.”

\-----------------------------------

“How the bloody hell did this happen?!” Lestrade spat blood out as he cursed and raged at everything and everyone in his general vicinity.

John grimly handed him a bottle of water and he washed his mouth out with it before taking a long gulp.

“Tell me everything before Khan gets here.” John frowned. “You might not get the chance after he gets ahold of you.”

\-----------------------------------

Lestrade was already climbing into the jump ship when Molly arrived in the room. Both were dressed in the formal Starfleet uniform of a deep grey color, the only differences between their outfits being the small patch of color on their chests indicating their divisions; medical blue for Molly and tawny gold for Greg.

John squeezed her hand as he helped Molly into the vessel, reminding Lestrade at the same time of the area in which he was to land and hide the small craft. As John ducked his head inside to buckle her in, Molly took a deep breath and the other doctor smiled encouragingly.

“It’ll be fine, Molly,” John reassured her. “He’s thought of everything. Really, I don’t see how one person could come up with so many likely scenarios.”

John shook his head in amused exasperation and Lestrade sighed as he peered past the blonde man.

“Where is he, anyway? He said not to leave until he got here but we’re ready and if we don’t go soon, we’ll miss our window.”

That window, of course, being the change of guard in the warehouse-like area where the other cryotubes were being held.

John glanced over his shoulder as he ducked back out of the craft and chuckled.

“He’ll be here. Surey by now you’ve noticed he has a bit of a flair for the dramatic,” he said with barely concealed amusement.

“Bloody drama queen he is,” Lestrade agreed, though he pitched his voice low enough that it was hard to hear.

Molly grinned at the men’s exchange, her eyes darting to the glass door, searching for Khan. She hated to admit it, but she was beginning to crave his presence. His voice soothed her and his touch… She couldn’t forget the feel of his fingers brushing across her hand in the lab. It was as if his touch had ignited a fire in her veins and she needed more. She craved more.

The petite woman shook her head slightly to dislodge her thoughts which were turning more inappropriate by the second. She couldn’t afford to be distracted today, not with such a huge task ahead of her and so much risk in it. She couldn’t lose sight of the fact that Khan was a murderer either, not matter how much she desired him or how obviously he wanted her in return.

John and Lestrade continued to talk, going over the plan again.

Finally, Khan appeared, and Molly caught her breath as he stalked through the glass doors and ducked his head inside the jump ship on her side, his face level with her own.

“Here,” he said, handing her a small, flat object. “Clip this inside your collar. It will relay your exact location, along with physical data, to the captain’s computer here. I’ll be able to see where you are and monitor your heart rate and breathing patterns from here.”

“Do you really think,” Lestrade started, but Khan silenced him with a glare.

“Yes, Lestrade,” he growled, “I do think it’s necessary.”

Molly grasped the tiny monitor in her hand for a moment, then looked back up at Khan who was watching her expectantly, his cold blue eyes assessing her. She smiled slightly, more like a grimace actually, and slid the clip onto the collar of her shirt, the cool metal of the device making the soft skin of her throat prickle with goose bumps. She gasped at the cold sensation and looked up to see Khan’s pupils dilate at the soft noise. She stared at him, mesmerized by the ever-changing colors in his unreadable gaze.

After a moment of tense silence, Molly’s eyes dropped to her lap and Khan finally moved, slipping his upper body back out of the jump ship and standing back, his arms crossed.

“Do not deviate from the plan. Get as many of the crew as you can this time because I can guarantee that the next attempt will not be so simple. If at any time, you are compromised, get out of there and report back here immediately. Above all,” he looked from Lestrade to Molly and back. “Do not get separated.”

The two people in the craft nodded and John retreated through the glass doors, followed by Khan, but not before he tossed one last lingering glance in Molly’s direction.


	7. Abduction

**Notes for the Chapter:**

> Thanks to AllTheBellsInVenice for looking over this for me.

Lestrade landed the ship, concealing it by activating the onboard cloaking device. It was well out of the way, no one would accidentally bump into the camouflaged craft. He climbed out first, rounding the ship to help Molly out. She smiled at the gesture, as it stirred something within her, maybe a memory, maybe not, but the action had a sense of rightness to it.

Molly looked both ways and then closed her eyes, picturing the map she’d stared at for hours the previous night. Her brown eyes snapped open and she smiled at Lestrade.

“This way,” she declared, pointing to their left.

“Lead on,” he replied and fell in step with her as she began to walk.

They traversed the streets of London silently, both concentrating on their task. Molly occasionally paused to examine the signs, but it was never more than a few seconds before she moved on, Lestrade shadowing her movements.

Finally, they arrived at the site where the rest of Khan’s, and their, crew was being held. They slipped into the building with little difficulty, the stolen identification cards Khan had presented them with doing the trick to open the doors. The next part was trickier.

Molly watched for any Starfleet personnel as Lestrade worked behind her, cutting wires to disrupt the live feed of the cameras from the room where the cryotubes were located. She momentarily panicked when she heard footsteps coming down the hall.

_Oh God, they can’t see him._

She pulled the door to the security room closed behind her and moved a few steps away from it, pretending to fiddle with her identification.

Molly looked up as the footsteps approached and smiled nervously at the man steadily getting closer to her. He stopped and held out his hand, giving her a charming grin.

“Well hello there, James T. Kirk, and you might be?” he said, managing to look both seductive and cheeky at the same time.

She smiled, her eyes flitting over his face. He was blonde, though not quite so much as Doctor Watson, and had clear blue eyes. She mentally compared them to Khan’s, and while his were bright and full of mischief, she found herself preferring the icy gaze of the man back on the _Vengeance_. Still, the man was handsome and young, very young to be wearing an officer’s uniform.

Molly looked him over more carefully. Wounds, barely healing, not more than a couple weeks old. Recognition dawned on her as she thought back to Khan’s presentation the day she awoke and her heart chilled.

She was speaking to Captain James T. Kirk of the _Enterprise,_ the man who was almost responsible for the capture of Khan the day he secured herself, John and Lestrade’s cryotubes.

She struggled to keep the panic from her face, and cleared her throat softly.

“Molly Hooper,” she replied, grasping his hand softly.

“Pleased to make your acquaintance Miss Hooper,” he said, pitching his voice low, attempting to be seductive. Molly almost laughed. He was a bold one.

“Doctor,” she corrected him with a smile. “Doctor Molly Hooper.”

“My apologies, Doctor Hooper,” he replied smoothly, casting another cheeky grin her direction. “I must’ve been momentarily blinded by your beauty to have missed such an obvious classification.”

She blushed prettily and smiled at him, but inwardly panicked.

_I’ve got to get rid of him._

“I haven’t seen you here before,” the man continued, and he looked back over his shoulder in the direction he’d just come from. “I’m here often, especially since…” He trailed off, looking a little dazed.

 “Are you alright,” she asked, and touched his arm lightly. He smiled down at her, coming out of his dark thoughts.

“Of course,” Kirk said brightly, before checking his watch. “Shit, I’ve got to go. I’ll see you around?” he asked hopefully, and Molly had to bite her lip to keep from laughing this time. Oh he was a ladies man for sure.

“Of course!” she agreed, adding a hint of flirtatiousness to her tone.

He grinned and winked at her then took off down the corridor, his footsteps growing more distant by the second. Molly fell back against the wall, a sigh of relief escaping her as Lestrade’s head poked out of the security room.

“Good thing Khan didn’t come. If he didn’t bash that man’s head in for just being in the wrong place at the wrong time, he certainly would’ve done if when he had the nerve to flirt with you.”

Molly huffed at the older man, and sighed.

“Worse than that, he’d have certainly recognized Khan. That was Captain Kirk of the _Enterprise._ ” Molly looked back down the hall where Kirk had disappeared.

“Come on, let’s get going before someone else pops in unexpectedly.”

Lestrade nodded and they proceeded quietly down the corridor, before coming to a metal door. Lestrade swiped his badge and it opened.

“Alright, we’ve got five minutes, give or take a few seconds before someone notices that badge shouldn’t be here and eighteen minutes before a squad arrives to apprehend us. Let’s get moving,” Lestrade said tightly, moving across the room towards the cryotubes, with Molly on his heels.

He gestured for her to go first when they neared, and she slipped past him, peering down into the tubes one by one. Khan had instructed her to check them for anyone she might recognize and give those tubes priority. She was starting to get discouraged when she finally looked down at a familiar face in the seventeenth tube.

The woman inside was dark, with kinky black hair and full lips. Molly had no idea who she was, only that she triggered a memory, and so told Lestrade to hook up the transporter device to her capsule. He did so quickly and efficiently, as Molly moved on down the line of tubes. After a moment, he looked up, his brow furrowed.

“There’s not seventy-two tubes here,” he stated, his eyes flitting over the tubes again, reassuring himself that he’d counted correctly.

Molly looked up and began to count, but he stopped her.

“There’s not, don’t count, we don’t have a lot of time left,” he checked his stopwatch, and called out the time to her.

“Six minutes down.”

She nodded, biting her lips and motioned to one of the tubes.

“Here, this one.”

A man was inside this one. He was thin and had facial hair which matched the light brown hair on his head. Once again, Molly had no idea who he was, but his appearance rang a bell in a deep part of her mind so she bade Lestrade to attach another device to his tube.

She found a third soon after, an older woman who had a kindly look, even in her drug induced sleep. She had short cut, light brown hair, which curled slightly and her skin was wrinkled with laugh lines. Molly felt a sort of daughterly affection towards the woman, and smiled down at her as Lestrade fitted yet another device to the capsule.

Suddenly, Lestrade froze, listening intently. He motioned for Molly to be silent and stood stock still, hearing things with his superior faculties that Molly couldn’t.

He hit the button on the device wrapped around his wrist and the three capsules disappeared, slowly fading out of sight. Molly’s eyes widened in fear as he motioned for her to hide behind a cabinet near the door.

The silence of the room was shattered abruptly by the wailing of an alarm and Lestrade cursed loudly, looking down at his timer as he grabbed Molly’s hand.

“Shit, we should’ve had another seven minutes,” he bit out angrily, as they dashed through the door and down the hall. They ducked into a side room as a lone figure in black dashed by, their face covered. Molly’s brow furrowed as she watched the retreating back, wondering who in Starfleet would dress in that manner.

Her thoughts were swiftly replaced though as Lestrade grabbed hold of her again and began running towards the door. She wasn’t nearly as fast as he was, and tripped several times trying to keep up.

They burst through the main door and looked both ways before Molly took off down the street at a run, with Greg right behind her. They made it several blocks before entering a dark alley. Molly’s chest ached but she didn’t stop. Suddenly, she was knocked to the ground, the force of the blow to her back taking the little breath she had in her away.

She rolled over, her eyes widening at the sight that met her eyes.

The man in black from the Starfleet building was engaging Lestrade in hand-to-hand combat and from the looks of things, they were evenly matched. Molly’s frantic brain froze in horror as she realized that the other man, now she could see the lines of his masculine body, could only be an augment.

She scrambled to her feet and took off, sprinting away from the fight and towards the safety of the jump ship. She was almost there when she heard the tell-tale sounds of pursuit behind her.

The petite woman didn’t stop running, but glanced behind her to determine if Lestrade had won and caught up to her. To her horror, she saw his attacker instead, gaining on her steadily. She weaved in and out of people, using her small size to her advantage.

She saw her chance when he was momentarily slowed by a group of slow moving pedestrians, and ducked into a dark alley. He passed by but she realized she’d made a monumental mistake moments later as she slipped into darkness induced by a liquid sedative, dark figures above her blurring into black.


	8. Recognition

**Notes for the Chapter:**

> Thanks to Onedayer for the TrekCheck! You're fantastic!

“Hello, Doctor Hooper. It’s nice to see you again, pardon my faux paus earlier when I referred to you as a Miss.”

_Well at least she’d meet her end at the hands of a polite person._

The cold voice echoed through the room Molly awoke to find herself in. It was stark white, clinical, almost like a lab of sorts, with only a table and several chairs, all metal, scattered around. The floors were concrete, polished to a shine, and the walls were a nondescript, endless white, with not even a single picture or window to break up the monotony of its sterility.

She was bound to one of those chairs, with what felt like a thick rope. As she tested her bonds, it seemed that they were more to hold her upright than to retrain her however.

She struggled to look over her shoulder, and cursed herself when it proved useless, as well as alerted her captors that she had awakened.

She blinked groggily in the bright white light that lit up the area as soon as she moved, a motion sensor activating it. She blinked again, her eyelids heavy from the drugs still coursing through her system. She fought the blackness, but it overpowered her, and she fell once again into a deep, dreamless sleep.

\---------------------------------

“You were supposed to stay together!” Khan roared, pinning Lestrade to the brick wall of an alleyway with a snarl.

The older man made no move to struggle, only wiggling enough that Khan’s fingers relaxed on his airway slightly. At his shoulder, John tried his best to pacify the raging augment.

“Khan, it isn’t his fault. They were attacked. It’s easy to get separated,” he pleaded, reasoning with the cold man whose hand had not left the other’s throat. Khan finally dropped Lestrade, turning his back to him as the man choked for breath.

“Easy to get separated?” Khan repeated in a growl. “Easy to get separated?!” He turned on Lestrade again, screaming at the man who now sat on the ground, braced up by the wall behind him.

“You let her out of your sight! And now she’s gone!!” Khan hurled the useless tracker at the wall, breaking the already fractured device into several pieces with the force as it struck.

“Calm down, we’ll find her,” John’s voice took on a soothing lilt, and Khan breathed deeply.

“How, do you propose we do that, Doctor Watson?” he replied sarcastically, pointing to the shattered bits of the tracker which would have given them Molly’s location. They’d discovered it when Khan appeared suddenly, his long coat swirling around him as he ducked into the alley where Watson had found Lestrade, rather the worse for wear, and tersely commanded them to follow him. He’d led them to the last place Molly’s tracker had been functional, and they’d unearthed it there, half buried in loose gravel of the alley, causing Khan to come unglued.

He was angry with himself for letting her go in the first place, cross with Lestrade for losing her, and above all, murderously furious with whoever had taken her.

The evidence was in her tracking device, her swift heartbeat transmitted to the ship for Khan to read, then the sudden slowing, caused by the injection of a sedative and then the abrupt stop of transmission, caused by the grinding of a heel into the device.

Khan’s jaw clenched. There was no way to track her unless perhaps they could hack into the CCTV that blanketed London’s streets. Speaking of which, they were still wanted and that same camera feed could be used to find them. He sighed.

“Back to the ship. We’ll awaken the three you managed to save and try to find a lead on Molly’s whereabouts.” He turned on his heel and headed back to his jump ship, leaving John to pull Lestrade to his feet and set off for the other.

\---------------------------------

“Ah, Doctor Hooper, awake again I see. Perhaps this time enough time has lapsed that the drug won’t lull you back into sedation. I am sorry, I fear we overestimated your dosage by a bit.”

Molly blinked in the light, pleased to find that her eyelids were no longer as heavy as they had been the previous time she was lucid.

“Who,” she began before coughing, her throat scratchy and raw. Instantly, a woman appeared from the shadowy corners of the room, bearing what appeared to be a glass of water. She pulled at Molly’s bonds and they fell away easily, giving Molly further proof that they had been meant to support her, rather than restrain her. The woman, a tall figure with brown hair and eyes and a bored expression, silently handed her the glass, which Molly took, eyeing suspiciously, and trotted back over to the shadow, disappearing from Molly’s view.

“Drink, my dear, it’s quite safe. Your throat is rather raw from your sprint and the after effects of the sedation. I apologize for that again.”

The voice was the same detached one from before, but now held a note of fondness in it, warming the cold tones with a bit of mirth. It pulled at a memory in the back of Molly’s mind and while she didn’t particularly like the voice, she trusted it. Besides, if whoever had abducted her wanted her dead, they could’ve easily disposed of her already.

With that in mind, Molly upended the glass, greedily chugging down its contents. The cool water soothed her parched throat and she smacked her lips, able to speak again.

“Who are you?” she asked the darkness, and was met with the appearance of another figure. This one was tall, and a man, who Molly quickly decided was the owner of the disembodied voice she’d been hearing. He was impeccably dressed in a rather old-fashioned three-piece suit. Molly had only ever seen one at a Starfleet gala, where the theme had been ‘The Good Old Days’. No, wait, that wasn’t true, she saw them often, didn’t she?

The man must have caught the conflict in her eyes, because he squatted directly in front of her and nodded.

“You know me, Doctor Hooper. Think! Throw away those useless memories you were programmed with and THINK!” His voice reverberated off the cold walls and Molly winced.

_Think. Okay, think._

Her brow furrowed. She couldn’t put a name to the man but as she studied him, he seemed more and more familiar.

“You should have an umbrella,” she blurted out, and clapped a hand over her mouth immediately. The man chuckled.

“Indeed, my dear, I should. Never went anywhere without one before.” He frowned, pondering. “No need for them now, really. I hardly leave this bunker.” He looked rather lost for a moment and Molly felt the urge to comfort him.

“Who are you?” she tried again, and he snapped out of his thoughts.

“Doctor Hooper, you need to listen to everything that I say and trust me explicitly, can you do that?”

Molly chewed her lip, looking at the man before her for a long moment. All she had to go on were a few feelings and distant memories, and, well, he **_had_** abducted her by force. Still, she nodded, hesitantly, but more firmly by the second.

“I trust you.”

In a blinding moment of clarity, she smiled, then repeated herself.

“I trust you, Mycroft Holmes.”


	9. Mycroft

**Notes for the Chapter:**

> Thanks Miz-Joely for the massive amount of edits on this one and to onedayer on tumblr for the TrekCheck. There's a lot of exposition in this chapter but I promise it's necessary and we'll get back to action and ust very soon!

“Concentrate. Do you see it? Every detail?”

Molly nodded and sucked in a surprised breath when the sharp point of an umbrella poked her in the stomach, just hard enough to grab attention, but not enough to truly hurt. She rubbed the spot ruefully and pouted.

“Ow, what was that for? I’m concentrating,” she whined. She crossed her arms over her tender midriff, protecting herself from further jabs. She couldn’t see them coming due to the contraption on her head. It was similar to a motorcycle helmet from the old days but covered her face to the nose and the top of her head, leaving the back open.

“You forget, I can see everything you are thinking with the help of that little device. Amazing the leaps technology has made during our little nap, though I have been informed that this particular bauble only works if you make your mind open to it; it cannot be forced. But, I digress. Oh, and I’d appreciate a little less of the, hmm, graphic images of my brother. Though I can almost assure you that you are most likely being generous in your imaginings.”

She giggled in spite of herself and heard a dramatic sigh from the man.

“I said less, Doctor Hooper. Less, not more. And you are definitely exaggerating; he is still human, even with the augmented DNA, do get a grip.”

Molly bit her lip and focused, once again calling forth the image of the pristine morgue, with all its nooks and crannies. She was filing away her memories in the many drawers and lockers, according to the technique described to her by Mycroft Holmes. He said that it was the same one that Khan – Sherlock - had once used, calling it his mind palace. She vaguely remembered that deep baritone voice uttering those words. She filed it away, along with all the other memories she retained of their former life.

Mycroft had explained the dire nature of their situation to her the previous night, after she’d awoken from the sedation. Something was terribly wrong. For one, Mycroft wasn’t sure who had awakened them, and for what purpose. The cryosleep was meant to protect them, when the catastrophe that he refused to speak of had struck, so long ago. It was his plan, and someone had reached into it, toying with their minds, making them forget the past and remember a false life.

Mycroft had overcome the implanted memories, his brilliant mind pushing them aside in search of the truth. He’d awakened his closest followers, stealthily pinching the cryotubes from Starfleet before they even knew they existed. For this reason, Mycroft, Anthea, and their two bodyguards were not missed from the total count of cryotubes. Not even Khan knew of their existence. Mycroft’s three assistants were all augments, but he himself had forgone the DNA change, citing his already superior mind and distaste for “getting his hands dirty,” as he called it with a derisive sniff. They discussed the pros and cons of the genetic alteration as they viewed footage of Khan making his way through the wreckage of that unfortunate Starfleet building not far from their present location, in the heart of London.

Mycroft had warned her not to fall into the habit of calling him Sherlock again, to even think of him as Khan. For though he was, in truth, Sherlock Holmes, the man he was now was a far cry from the consulting detective Molly had known in a past life.

Mycroft pursed his lips together as he explained that they should have awoken a mere twenty years after the disaster that forced his hand and caused them to be lulled into their long sleep. Somehow, twenty years turned into much longer, and they were awakened into an unknown world by an unknown force. Mycroft was not even positive he had been the first to rouse from the long rest, having only been able to catch a glimpse of the other tubes when he nicked his own followers from under Starfleet’s figurative nose. He hadn’t been aware that his own brother was so changed until information surfaced of a John Harrison being utilized by Admiral Marcus, whom Mycroft had taken a keen interest in due to the illicit nature of his activities.

Ever the mover, Mycroft had quickly adapted to his surroundings and sought out those to whom he could offer his services. Now, he was covertly working his way up through the British government once more, his intelligence quickly bringing him to an understanding of the new times, and the new threats that occupied the new world. Mycroft worked from a bunker, deep under the city, one left from the wars that had damaged the world during the time they slept.

He was a ghost on record, Molly found, and she had laughed ruefully, noting to an amused Mycroft that he should be perfectly comfortable as such, because he had been in their own time as well. No one had known where the true power in the British government had lain, and it appeared as if things were getting back to normal, in that area at least.

He’d carefully explained to Molly that she was to by no means try to get his brother to regain his memories. Mycroft was convinced that Khan was a whole different personality within Sherlock and that if his past self were to resurface abruptly and realize all the things he had done as Khan, that it could break him. He taught her how to phrase things, to echo her past self, in the hopes that he would gradually reconcile the two personalities, though Molly had considerably less hope of that than Mycroft.

In truth, knowing what she did, Molly wasn’t sure exactly what she hoped for. On the one hand, Khan had committed terrible acts, was a criminal of the worst kind, even though in his own mind, he was the hero. Sherlock had never considered himself a hero, but Khan was convinced he was one. The two men were so distinct, so at odds with one another, though both brilliant and out of step with the rest of the world. On the other hand, Khan desired her, and Sherlock had never more than considered her useful.

Molly bit her lip. She was a small bit selfish as well. She was only human, and it was a very human emotion, but she felt terrible for the thought even crossing her mind. Khan wanted her. That much was painfully obvious. She wasn’t sure exactly why he wanted her, but there was no doubt that he did. But now, with the theory that he was merely a separate personality in Sherlock’s body, Molly wasn’t sure what to think. When Sherlock came back, if he ever did, would he want her? Or would it be like that vague pain she felt in the recesses of her heart when she concentrated on memories of their past? A brush of lips across her cheek, red lipstick and a red wrapped gift, the smell of coffee and cigarettes, an unconscious wish to hide her too small breasts. She didn’t know.

Molly wasn’t sure who would hurt her more, Sherlock or Khan.

After a full day of memories and training by Mycroft, he reluctantly told her that she would have to go, before Khan found them. Instructing her on the lie she would tell to cover her absence, he fondly - well fondly for him - bid her farewell, leaving Anthea to show her out and drop her where Khan was sure to find her.

As she turned to walk away from him, he reached out and grabbed her hand, looking at it, a bit stunned that he had done so.

“Doctor Hooper, I assure you, whatever fondness he may show for you now, it has always been there.”

With those words, Molly found herself back on the very street she had been taken from, alone.


	10. A Last Minute Addition

**Notes for the Chapter:**

> Big thanks to Miz-Joely and Onedayer for the beta and TrekCheck!

Molly blinked several times, trying to get her bearings. Her eyesight was a little fuzzy and she assumed it was an aftereffect of the device used to transport her back to the street. Mycroft had banked on Khan keeping an eye on her last known location, so all Molly had to do was wait until he arrived to claim her.

A movement in the shadows caught her attention and she tensed, ready to break into a sprint if need be. A soothing voice stopped her flight, calling out her name.

“Molly, it’s alright. Mycroft sent me to watch over you.”

Molly’s brow furrowed. He hadn’t mentioned any such plan, but the man was rather tight-lipped, leaving a lot of the explanation of what she should and should not do to his assistant, Anthea. Though she hadn’t mentioned a companion either. Molly watched with eyes narrowed as a slight woman with dark hair and scarlet lips, dressed in a Starfleet uniform which was a bit worse for wear, stepped out of the shadows.

“Quickly now, this is the story you will tell Khan. You were captured by Starfleet. I am an augment and one of Khan’s crew who was awakened by Starfleet for study, and escaped their grasp, rescuing you at the same time. You brought me here so that he could find us.”

She stopped and smiled, though Molly couldn’t help but think it failed to be reassuring. Her lips were too red, her hair too perfectly kept, nails with a posh manicure.

“How do I know you are sent by Mycroft? He didn’t mention you.”

Molly studied the woman as her expression turned bored, though she tried to hide it with another forced smile.

“You can ask any questions you like, but Khan will be here soon. At least stick to the story for now, and I can prove myself to you at a later time. My name is Irene, by the way.”

Something about her though, tickled the edges of Molly’s memory. Her face was unfamiliar but her name rang a distant bell in Molly’s head. She couldn’t tell where she’d heard it, but it was important somehow. Molly made a snap decision then, not taking the time to weigh out the pros and cons of trusting the woman. She could be working with Mycroft or not, either way, if Molly was going to discover who she was, then she needed to be close. Surely with Khan, Greg and John around, she could do no harm to them or the ship.

Her thoughts were cut short though, by a sudden shout. She turned to see Khan appear, with John hot on his heels. The augment did not slow, swiftly stepping in front of Molly and catching the other woman by the throat.

“You have thirty seconds to convince me not to end your life. Speak.”

It wasn’t the woman whose voice rang out however. Molly’s hand closed over his and pried it away from the woman’s throat, as she spoke rapidly, moving around to where she stood between Khan and Irene, both of whom were looking at her as if she’d gone mad.

“This is Irene. She rescued me from Starfleet, she helped me escape. She’s one of us, an augment and part of the crew. I,” she faltered. “I remember her. Not her face, her voice maybe? Something about her…” she trailed off, looking distinctly uncomfortable.

Khan looked from one woman to the other several times before sighing deeply, and running a hand through his hair.

“Alright,” he finally replied, speaking directly to Irene. “You will be allowed to come with us, but until you prove trustworthy, you’ll be under constant surveillance.”

She pursed her lips but nodded, not contesting Khan’s conditions. Molly breathed an inward sigh of relief, before furrowing her brow, realizing exactly what she’d just done. Because of her, an unknown factor had been added to the equation. She hoped that she hadn’t just made a terrible mistake.

\-------------------------------

Khan kept his eyes on the woman before him as he brought his wrist up close to his face, in order to use his wrist communicator. He had left Lestrade in charge as soon as Molly had shown up on surveillance; John had barely made it into the jump ship in time to ride along, Khan was in such a hurry to get to her.

“Lestrade,” he barked into the com. “Have Billy ready with an ankle monitor the moment we come aboard.”

“Billy?” Molly’s soft voice questioned, and Khan smiled, throwing John a meaningful look, and turning his back on the newcomer once his second in command had assumed a defensive position next to Irene. Khan took Molly’s arm and moved her several steps back from the other two as he spoke, subtly running his hands over her to check that she was really fine.

“Yes, Molly. Billy is one of the ones you managed to save.” He smiled down at her, watching a blush spread across her face at his praise.

“It wasn’t me. Greg did all the work. All I did was point,” she stammered, making Khan frown in confusion, and then annoyance as he realized who she was referring to.

“Do not belittle yourself, Molly Hooper,” he snapped, reaching out to close his fingers around her jaw and lift her face to make her look at him directly. “Never do that,” he reiterated, watching her carefully.

He’d been frantic with worry, though had attempted to keep it hidden from the other people aboard the Vengeance. Khan had been irritable and moody, often losing his temper at the slightest thing and the both Watson and Lestrade had tiptoed around him ever since Molly had gone missing.

Lestrade had taken the brunt of Khan’s temper, and the captain had to admire the self-control he displayed, never lashing back when he was berated for small errors, or, on several occasions, something that wasn’t even under his control.

The new crew members had been awakened, and John had figured out a more efficient way of doing it, which meant that they woke far more rapidly than when Khan had woken Watson, Lestrade and Molly.

The first to awake was a young man, sallow and thin, with bright blue eyes. He’d identified himself as Wiggy, to which Khan raised a brow, causing the man to correct himself and give his full name, Bill Wiggins. Wiggins was a hacker, it turned out, and Khan was hopeful that once he learned how to use the newer tech aboard the _Vengeance_ , that he’d be able to patch into the hidden archives of Starfleet and obtain some useful information.

Next, a young woman who had instantly clashed with Khan. When Khan stalked into her quarters, arrogantly identifying himself as her captain and rescuer, the olive skinned beauty had pursed her lips and shook her head at him, refusing to acknowledge his authority, until Lestrade had entered the room as well and affirmed that he was loyal to Khan. She’d given her name, Sally Donovan, to Lestrade, apparently instantly trusting the grey haired man. When she’d regained her strength well enough to walk the ship, she’d attached herself to Lestrade’s side, preferring to help him in his duties than to deal directly with Khan, which suited the captain.

The last to become lucid was the older woman. Barely an hour before Molly had been located, she’d blinked awake, immediately attempting to sit up and complaining about her hip, and how it always hurt when it was going to rain. Khan had genuinely smiled for the first time since Molly had been taken, and gently told the woman that it couldn’t possibly be about to rain, since they were in space, and there was no atmosphere. The brown haired lady had put a shaky hand to her mouth when he showed her to the window, and muttered about how things were different in her day.

He’d been with her when Lestrade had buzzed his communicator, excitedly informing Khan that Molly had shown up again in the alley where she’d disappeared from. Immediately he’d taken off, running through the ship, shouting to Lestrade that he was in charge until he returned, knowing that Watson was sleeping in order to be rested enough to take the second watch. To his mild surprise, John arrived at the jump ship just after him and dove in just as Khan was preparing to depart, hiding a yawn behind his hand.

At his commander’s raised brow, John had merely shrugged and mumbled something about not getting his impulsive arse killed and Khan had turned his head to hide his amused grin, since he, as an augment, was certainly less likely to get injured than John, who was still a mere human. Still, the sentiment touched him and he didn’t complain or order the fair haired man stay behind.

Now, Khan looked down at the woman he hadn’t been sure he’d see again. He moved closer to her, invading her personal space and brushed a stray lock of hair from her face, gently running his fingers over her cheek and down to her jaw. He leaned closer, maintaining eyes contact as he stood close enough to her to feel her quick breaths on his own lips and see her eyes dilate rapidly as she stared up at him.

“We need to get back to the ship,” he announced, straightening suddenly, and turning on his heel. He heard her ragged intake of breath behind him as he stalked away from her, back towards the others, and grabbed Irene by the upper arm, pulling her along as Molly and John fell into line behind, and the headed back to the jump ship.


	11. Data Crystal

**Notes for the Chapter:**

> Thank you to my wonderful friends! MizJoely for the beta and Onedayer for the TrekCheck!

Khan sprinted through the ship, in the direction of his quarters.

The last few days had been quiet, with no opportunity for action. Starfleet had spirited away the remained cryotubes, and they hadn’t been able to uncover their location as of yet. Just this morning, they had their first breakthrough since Molly had been found and Irene had come aboard.

Irene. Khan slowed as his thoughts turned to her. She had been the picture of innocence… well perhaps that wasn’t the right word to use. She was fiercely intelligent, especially when manipulation was concerned. She’d sweet talked several Starfleet guards into disclosing varying information, none of which proved incredibly helpful, throughout the past several days. She still wore her tracking device, as Khan hadn’t come to fully trust her. The woman, as Khan had taken to calling her in his mind, was helpful, doing anything he asked without hesitation. She was knowledgeable about the newer technologies, as well as a wide array of other topics, and eager to please.

_Too eager to please_ , Khan thought with some distaste.

Irene had been very open with her flirtations with him, not making any attempt to hide her sultry innuendos when she spoke to him. Khan had frankly been a bit caught off guard by her boldness with him. She was intriguing and admittedly quite beautiful, but there was a coldness there that made him wary of her. Oh, there was passion and attraction to be sure, but none of the warmth that emanated from Doctor Hooper.

The quiet little doctor had been like a shadow ever since she’d returned, slipping out of the room quickly whenever Khan entered, and mainly sticking to her quarters. They had spoken briefly her first day back, as he questioned her about her time away from them. She’d been evasive, but not overly so. Mostly she said that she couldn’t remember a lot of her captivity due to being sedated. Khan wasn’t certain that was the whole story, but he knew that Molly wasn’t deceptive by nature and so let it slide, deciding that when she wanted to say more, she would. The rest of their conversation, well, Khan tried not to think about it, as it was difficult to keep from being aroused by the memory.

\-------------------------------------

_“Molly,” Khan stepped inside of her quarters, “are you all right?”_

_She looked up in surprise, crossing her arms across her chest with a yelp of alarm. She’d been in the middle of changing clothes, her shirt tossed on the bed as she stood in the middle of the room in her trousers and bra with her feet bare._

_“What are you doing?!” she shrieked, her face turning an alarming, endearing, shade of red._

_“I’m inquiring after your well-being. Isn’t that what I’m supposed to do?” he replied, his smirk showing that he knew exactly what she meant by her question. He continued towards her, letting the door slide shut behind him. His long strides brought him into her personal space quickly, and he looked down at her, eyes darkening with arousal. Without another word, he tangled his fingers in her hair, pulling to tilt her head up as he covered her mouth with his own._

_Molly gasped against his lips, and he took the opportunity to slip his tongue into her mouth, walking her back to press her against the wall, trapping her between it and his body. Her hands came up to clasp around his neck and she returned the kiss with equal fervor. The moment Khan’s hand came into contact with her breast, teasing her nipple through the material of her bra, Molly jerked back._

_“What the bloody hell do you think you are doing?!” she asked again, this time shouting at him. He stepped back slightly, dropping his hands, but remaining in her personal space._

_“I was kissing you, obviously,” he replied, smirking at her. “And I’d venture to say you enjoyed it,” he said glancing at her breasts pointedly. Her nipples were taut and visible through her bra, and her skin was flushed._

_“Get out!” she yelled at him. “Get out!”_

_Khan’s expression turned cold and he leaned closer to her._

_“Why are you fighting it, Molly? We both know you want me. Why not just give in? I promise you, I can pleasure you in ways you can’t even begin to imagine. But I won’t take you until you ask for it.”_

_Her breathing was heavy with arousal and anger._

_“I’ll never do that.”_

_“Oh, you underestimate me, Doctor Hooper. I don’t intend to play fair.”_

_He turned and left the room as quickly as he’d come, not stopping until he’d reached his private suite of rooms, where he’d collapsed onto the bed, ripping off his clothing, and taking himself in hand, stroking roughly until he came hard with Molly’s name on his lips._

\------------------------------------

Khan sighed, pacing back and forth in his quarters anxiously. The only really good news since that day had been that Billy Wiggins had proven his worth as a hacker, finally discovering a useful bit of information that morning. A carrier was to be dispatched in San Francisco to deliver orders concerning the remaining crew. The Starfleet Officer would be carrying a data crystal with vital information, and his orders were clear, saying that he was to protect it at all costs and that he was authorized to kill anyone who tried to detain him or obtain the crystal.

Those orders were all Khan had needed to know that the information contained on the crystal would be highly useful to them, and he decided to go after it. His initial plan had been to go alone, unwilling to trust something of such importance to another, less capable person, but Watson had become belligerent, insisting that Khan would not be setting foot off the ship without the company of his First Officer. Khan had reluctantly agreed, seeing that the good doctor’s mind would not be changed. He assigned command of the bridge to Lestrade for the time he would be gone, and mapped out a strategy with Watson, deciding that divide and conquer was their best option.

Now, they waited.

\-------------------------------

Billy kept constant watch on Starfleet communications, his computer a ghost on the network, waiting for confirmation that the messenger had departed to complete his task.

“Got ‘im!” he yelled delightedly into his communicator. “Leaving headquarters 2023 en route to 3407 right now! You can intersect him at,” he paused, squinting at his screen, “Bridgeway, in exactly 14 minutes!”

He heard Khan’s booming voice confirming and hurried footsteps, and leaned back, pulling up surveillance video of the street he’d mentioned. Keeping an eye on the screen, his brought his communicator back up to his mouth and glanced over to Lestrade and Donovan who stood a bit away from him. He muffled his voice with his hand, making sure that neither of the two could hear him.

“Doctor Hooper, they’re leaving, you best come on if you want to keep an eye on things.”

\---------------------------------

Molly had been avoiding Khan as much as possible, hoping to avoid a repeat of her first day back aboard the _Vengeance_.

She’d been so close to giving in and letting him take her. Molly had long ago admitted to herself that she wanted him badly, and was ill equipped to resist his determined advances. She was reluctant to let go of her self-control though, knowing that it was her duty to help him remember his former self, and that when he did, he might not want her like he did presently. It was a dilemma, one that Molly wasn’t sure she’d ever resolve.

When she heard that he would be going to the surface that day, she’d asked Wiggins to let her know when they left so she could go to the bridge and join him in keeping an eye on their captain. Wiggins had taken a shine to her, calling her “the missus,” which made her blush and chide him gently. He’d chuckled and agreed to her request, remarking that it would be easier if she just shared Khan’s quarters and stopped pretending that wasn’t where she wanted to be, a statement that made her gently hit him upside the head and scold him for being indecent. His cheeky grin let her know that he was in no way regretting his words though, and she’d sighed, giving it up as a lost cause.

She sprinted through the ship, making the journey from her quarters to the bridge in record time. As she stepped onto the bridge though, the sight that greeted her made her heart stop cold. Lestrade, Donovan and Wiggins were all gathered around the computer screen, shouting at it.

Lestrade looked up as she entered and his face frightened her with its intensity.

“Molly, get a medical kit!” he shouted at her. “John is down and Khan is fighting. We’re going down.”

She immediately turned and fled the bridge, heading to the medical bay with Lestrade hot on her heels. They passed quickly through the Sickbay, grabbing up the kit, and made their way to the transporter pad, where Donovan beamed them down to the surface, one street away from the action. They ran as soon as they hit the ground, with Lestrade outpacing Molly easily.

The first thing she saw when she turned the corner was Khan with a man’s head between his large hands. His victim was screaming, terrified, and Molly’s screams replaced his as Khan crushed his skull, dropping the body lifeless to the ground.

**Notes for the Chapter:**

> On Tumblr? Me too!! Find me @ liathwen.tumblr.com (hey hey, no teasing about the sucky url, I didn't know!)


	12. Friendly Conversations

**Notes for the Chapter:**

> Super thanks to mizjoely for the edits and encouragement!

“Molly, listen,”

“No, John, I won’t listen. He’s cruel and inhuman. How could I love a man like that? He’s not even a man, he’s a monster!”

Khan stood outside the medical bay where Molly was attending to John’s wounds from the fight. His fists clenched at his sides, anger and pain coursing through his body. He’d done the only thing he could do against a powerful adversary.

He ground his teeth together, furious at the turn of events. When he and John had arrived at the designated spot, only to find the messenger already dead and the very same augment who’d fought Lestrade before and given chase to Molly standing over the hapless Starfleet Officer’s body, Khan had seen red.

He’d lunged at the man, grappling with him as they fell to the ground, and for the first time since he had awoken, Khan had felt the fear of having an adversary who was equal to his strength. In a moment where his enemy had broken away, slamming him against the brick wall, Khan looked up to see the man catch John’s left arm in his grip and snap the bone in half. The blond man yelled out in fear and pain, and Khan was up again, lunging at his enemy in fury, pounding him into submission.

He caught the man’s skull between his hands and pressed, ending him in the same way he’d ended the pitiful Marcus. Khan looked up from the body when the screams of a woman met his ears and instantly his heart sank as he saw Molly standing there with Lestrade, the medical kit falling from her hands to the ground as she watched him.

“Molly,” he’d said, taking a step towards her. A groan from John drew their eyes from each other and Molly had gone into medical mode, swiftly binding his arm and helping him up as Lestrade searched the body of the augment and found the data crystal secured in the inner pocket of his coat. There was no other items on the body and they all limped back to their transport, metaphorically licking their wounds.

Molly had refused to speak to Khan, shying away from him as they carried a dazed Watson to the sickbay. Khan left, only to overhear Molly’s words drift to him from inside the room. His jaw clenched, and strode away, heading to the bridge to bark out orders and hand the crystal over to Wiggins for decoding.

\----------------------

“You might be better off if you take a rest in your quarters,” John remarked as Khan angrily punched on a display screen. “And by you, I mean all of us.”

Khan looked over his shoulder at the man standing behind him, his mouth twitched with a suppressed grin.

“John,” he affected a bored tone, “shouldn’t you be in the sickbay or something?”

“Why, this?” John motioned to his broken arm, comfortably resting in a sling. “Nah, it’s merely a flesh wound sir,” he grinned at his commanding officer. “Besides, you looked like you could use some help,” he said in a lower tone.

Khan’s brow furrowed in confusion before John subtly motioned to Irene, who was hunched over a screen not far from them.

“I’ll give her one thing, she’s persistent,” John muttered under his breath and Khan nodded his agreement before turning back to his screen.

The sultry brunette had barely left Khan’s side, fussing over him, brushing her body against his, making small talk, flirting. She’d even had the nerve to shiver and imply that she’d like Khan to keep her warm, her words leaving no room for doubt in what way she meant. Khan was saved from having to reply by the loud sound of Sally gagging behind them.

John jerked his head towards the door and folded his good arm across his chest. “Go on, we can handle things up here. You need time to rest.”

Khan nodded curtly at his second and left the room, secreting himself in his quarters to think over the day and wonder where it went wrong.

\-----------------------

A few hours later, Molly was startled by the sound of her bedroom opening. She looked up and saw John standing timidly at the door.

“Knock, knock, you busy?”

Molly smiled tiredly at him. “No, come on in. But John, no more talk about what happened earlier, yeah?” She passed a weary hand over her face as the blond man seated himself next to her on the edge of the bed.

“Molly please, you’ve got to hear me out on this one. He really didn’t have a choice. The man was an augment, fast, strong, almost as fast and strong as Khan, and he’d already incapacitated me. It was kill or be killed and Khan did what he had to, Molly. Think about it. If someone were to get past Khan, they could get to us. To you. Now I don’t know much, but I know that man would take on hell if it meant keeping you safe.”

Molly blushed and focused her gaze on her lap, where she twisted her fingers together self-consciously.

“It’s all of us, John, he wants to keep all of us safe.”

“Pardon my rudeness Molly, but it’s not all of us he thinks of when he’s in his bunk at night.”

They shared an awkward laugh but Molly’s died off first.

“Are you sure it isn’t Irene he’s thinking of?”

John turned to her, brows raised.

“Molly Middle Name Hooper, are you jealous?” he said, an exaggerated expression of surprise on his face. “What is your middle name just in case I ever have occasion to do that again?”

“Elizabeth,” she said, holding in a giggle.

“Molly Elizabeth Hooper, are you jealous?” he parroted back at her, a roguish grin lighting up his features.

“No, no,” she said, trailing off. “Well maybe a bit. But you know, I just, there’s just an odd feeling I’ve got about her.”

John nodded sagely, staring off into the distance. “I know what you mean. There’s something about her. Like if you take a hammer to that pleasing outer part of her, you’ll find muck underneath.”

It was Molly’s turn to look at John in surprise. “I thought you liked her. You been hanging around her an awful lot.”

John shook his head, chuckling. “Nah, I’m just trying to keep her off of Khan. Poor man, she’s determined to get to him and he’ll have none of it.”

“Are you sure?” Molly asked, looking down at her hands again.

“You’re being irrational about all of this. Trust me, Molly. Khan knows better than to be blinded by a pretty face and you’re being too hard on him for doing what any one of us would have done.”

**Notes for the Chapter:**

> I love your comments!


	13. Wine

**Notes for the Chapter:**

> Huge thanks to miz-joely for the beta and onedayer for the TrekCheck!

“She doesn’t deserve you.”

Khan stiffened and pulled his head from his hands as the sultry voice drifted in from his door.

“What are you doing here?” he growled angrily. He was in no mood to deal with Irene’s advances. He’d lost Molly, perhaps for good since she refused to see that he’d had no other choice.

“Wiggins sent me to tell you it’d be a while before he could crack the code on the crystal and that you should think about getting some rest.” She stepped farther into his room and he saw that she held a bottle of wine in one hand and two glasses in the other. She’d taken to wearing an old-fashioned riding crop hooked onto her belt, saying that if she couldn’t have a phaser, which Khan had forbidden, that she should have some way to protect herself and that that particular item had felt right.

“Wiggins didn’t say the last part,” Khan frowned, wanting nothing more than to be left alone with his thoughts, his frustration. No, he wanted nothing more than to bury himself in Molly, to lose his cares in the throes of ecstasy. Unfortunately, the object of his affection would have nothing to do with him. He felt his anger resurface as he watched Irene moved closer to him.

“No, you’re right, I did,” she said, holding the bottle towards him with a slight smile on her scarlet lips.

Khan sighed, eyeing her tiredly. “What do you want, Woman?”

She chuckled softly, and shrugged. “I can help you. You’re angry, frustrated, stressed. I can help, I can relieve some of that,” she paused and licked her lips, “tension.”

Khan’s brow furrowed as he looked at her. She was proposing that he use her to relive his stress. He couldn’t deny that the idea was appealing. Not nearly as much as it would be with Molly, but he had to admit that Irene was beautiful and willing to be with him, knowing that it was strictly sex, that he cared for another.

A woman who would have nothing to do with him, even though he’d done nothing wrong, Khan’s mind whispered. He frowned and straightened, sweeping his gaze over Irene with renewed interest.

“I’m listening.”

She smiled widely, and crossed the room to within a few steps of him, holding out the bottle again.

“I thought you’d see reason. Here, I brought wine.”

“I don’t want any,” he began, shaking his head, but she cut him off, moving into his space and pressing the bottle into his hands, and herself against his side. She produced an opener from her pocket handed it to him, switching the glasses to her other hand.

“Hush,” she whispered, putting her newly freed index finger to his lips. “You said I could help you.”

“I, no I didn’t,” he protested, realizing that he was opening the bottle without thinking about it. It produced a pop and she smiled, knowing he was caught.

“Let me,” she said, taking the bottle from him and turning her back to set the glasses on a low table before filling them both. She straightened and turned round, handing him one.

“She doesn’t appreciate you, she doesn’t see all you do for her,” she said, clinking her glass to his.

“It doesn’t matter,” he muttered, angrily. She put her hand on his upper arm, sympathetically patting him. She sighed and chewed her bottom lip, an action that caught Khan’s attention.

“I know I’m not the one you want, but let me give you what she won’t tonight,” she whispered, gazing up at him from beneath long lashes.

“Woman,” he warned, still warring with his conscience that told him he should wait for Molly.

“Shh,” she whispered seductively, “let me do this for you.”

She turned her back to him, setting her glass down as her hands went to the back of her short Starfleet issue dress, catching hold of the zipper. She turned back to him, stepping back several paces to let him watch her as he sipped his wine.

Khan watched her, jaw clenching as images of Molly filled his head. He shook it, annoyed. He was determined to get his infatuation with her out of his system and focus on the stunning woman in front of him. Irene was indisputably beautiful, sensual and lithe, a tiger in a woman's body. Khan took a long gulp from the glass of wine she'd poured as he watched her disrobe slowly, slipping her dress down her body to reveal that she wore no bra to accompany the black lace knickers and garters which held up the black thigh highs, disappearing into her heeled boots.

He smiled appreciatively, batting away thoughts of Molly and how sweet she looked in her bra and trousers just a few days before. He refused to pine after a woman who did not return his feelings. Khan drained his glass, hoping it would help him relax and drive away the ridiculous feeling of guilt that was creeping its way through his gut. Why should he feel like he was hurting Molly? They weren't together, as she'd refused his advances over and over in the time since she'd awoken from cryosleep.

But he just couldn’t. He couldn’t watch the gorgeous woman before him one second longer. He wouldn’t betray his feelings for Molly that way, he wouldn’t do something he’d despise himself for later. Khan opened his mouth to tell her to stop, to leave but no sound came out. He looked down at his empty glass, then back up at Irene and back down, his eyes widening as he made the connection. He dropped to one knee, the glass falling to the door and rolling as Irene stood watching him with a knowing smirk.

“You,” he stuttered out, his voice cut off by the sudden crack of the crop across his face, contacting his cheekbone dangerously close to his eye.

“You fool,” Irene snarled, her gaze icy as Khan gasped for breath. “Did you really think that I was so taken with you?” She smiled coldly. “It’s a mistake you won’t live to regret I’m afraid.”

She reached to her dress pocket and pulled the data crystal from it.

“So much trouble for such a petty thing,” she mused as Khan made a feeble grab for it, and missed.

“I’m afraid Wiggins is decoding a fake. I switched them when he wasn’t watching. Honestly, you need to teach your crew to keep a better watch.”

She pulled her dress back on, watching Khan closely as he writhed on the ground in pain, his moans barely audible through his seized throat. She put a finger to her mouth in contemplation and then quickly reached under her skirt to wiggle off the lacy knickers. She tossed them casually on the floor next to the table and grinned. Walking over to him, Irene stepped on his chest, the heel of her boot digging harshly into his breastbone as she leaned over slightly, giving him full view up her skirt as he lay whimpering.

“You should’ve stuck with Doctor Hooper, she’s far more loyal than I ever would be,” she whispered with a smirk.

“You can’t go anywhere,” Khan rasped, trying to catch hold of her ankle which she deftly pulled back as she shook her head at him. “You’ve got a monitor.”

She looked down at her wrist in mock surprise. Khan had switched the monitor to her wrist from her ankle just the day before when she complained that it got in the way of her wearing boots. Now he realized that he’d sent her to fetch it and had not checked it, as he’d been called away by Lestrade just as he placed it on her.

A mistake he was definitely regretting now.

“There you go, love. I knew you’d figure it out,” Irene cooed at him and Khan grimaced from a combination of pain and anger at himself.

“Well, I would stick around,” she said over her shoulder as she walked to the door, “But it’s going to get ugly when that poison starts to metabolize, and I’d rather not see that if it’s all the same to you.”

She stopped at the door and smiled at him.

“If it makes any difference, it’s nothing personal. Just business darling, just business.”

With those words, she left, closing the door behind her, leaving Khan to writhe on the floor in agony, his stomach burning as the poison worked its way through his system.

\----------------------------

“You’re right, I’m not being rational about this.” Molly sighed, her head in her hands as John patted her on the shoulder with his good arm.

“Go talk to him,” the doctor encouraged. “You know it would mean the world to him if you told him that you understand. And he really had no choice,” John assured her solemnly.

She nodded, standing. “All right, I’ll talk to him.”

“Last I saw, he was headed to his quarters,” the doctor said, standing as well. “He’s probably still there. You can talk to him privately.”

“Okay,” Molly replied as they moved towards the door. “Thank you John.” She gave him a one armed hug, careful to not jostle him much. He was under powerful medications and so wasn’t feeling the pain from his injury, but she didn’t want to exacerbate it.

They parted at the door and Molly walked quickly towards Khan’s rooms, trying to push down the nervousness that bloomed in her belly at the thought of being alone with him in his quarters.

Her brow furrowed as she almost ran into Irene, rounding a corner.

“Oh, I’m sorry,” she sputtered, as the other woman moved to go around her.

“It’s quite all right Molly,” Irene said with a smile. Molly watched for a second as she walked away, trying to put a finger on what seemed off about her, but gave up, assuming it was her usual odd feeling about the woman.

She arrived at Khan’s room and knocked, twisting her hands together nervously. When he didn’t answer, she turned to go, but stopped short at the pained moan that sounded from inside. She punched the button to open the door and nearly screamed when she saw Khan collapsed on the floor, his eyes fluttering closed.


	14. Aftermath

**Notes for the Chapter:**

> So sorry that I left you hanging for so long!! I had some personal issues to work out, but hopefully I'll be back to updating more rapidly now. Thanks for your patience and thanks to miz-joely and onedayer for looking over this for me!

One look around the room told Molly what she needed to know. A bottle of wine, two glasses, one empty, one full, and a pair of black lacy knickers on the floor. Her jaw tightened.

“You idiot!” she screamed, both angry and terrified that he was going to die. Irene was an augment and so must know the dosage of poison that must be given to take down a man as powerful as Khan.

She sprinted to his side and dropped to her knees next to him, not registering the pain in her legs as she did so. All her focus was on the man on the floor before her as her fingers closed around his wrist, praying silently that there was a pulse still there.

It was weak, faint, but still detectable and she dropped his hand to shout into her communicator for John to get to Khan’s room immediately with a full med kit and a stomach pump and for everyone else to catch Irene before she could leave the ship, as Molly was sure she intended to do.

After getting her instructions through, she checked Khan’s pulse again, and was dismayed to discover that it was even lighter than before. In desperation, her eyes flicked over his chest and up to his lips. She could perform CPR but there was a good chance that the poison he had swallowed still lingered in his mouth.

The second his breathing stopped, all thoughts for her own safely fled and Molly gave a cry of desperation, clambering onto his hips to straddle him, and pounding on his chest with all her force. She knew it was highly unlikely that she’d do any damage to his augmented torso, so she held nothing back, beating on his chest before leaning down and covering his nose, forcing his mouth open, and breathing deeply into it. She repeated the CPR over and over, feeling her limbs beginning to deaden from the poison she was ingesting from his lips.

She bit her own lip until it bled, the pain giving her a last bit of clarity as John came running in. She told him in slurred tones that Irene had poisoned Khan, and to pump his stomach before collapsing.

Her last thought before blackness overtook her, was that she’d kill Irene herself if she ever saw her again.

\--------------------------

Khan came to with a roar, sitting bolt upright in his bed and blinking rapidly in the bright white light.

John was immediately by his side, looking exhausted and worried. Khan’s brow furrowed as he snapped out questions while John attempted in vain to examine him. He could feel lingering weakness in his body but knew that his system was cleansing itself. He was sweating as his immune system worked in overdrive to rid his body of the poison that had already been absorbed before John had gotten to him.

“Where is Irene?!” was his first question, and John sighed.

“She got away. Took one of the jump ships and made it to Earth before Lestrade and Donovan even got to the Bay.” He kept glancing to a spot behind Khan, and the sadness in his eyes was easily readable. Khan assumed it was because of the doctor’s concern over the situation.

Khan surveyed the medical bay and realized something was missing and his stomach dropped.

“John,” he asked quietly. “Where is Molly?”

John’s eyes flitted back to the space behind Khan once more and the augment slowly turned to follow his gaze.

His heart stopped for the second time in as many hours when he saw what John had been looking at.

Molly was nestled in a crisp white bed identical to his own under a mountain of blankets. She was completely devoid of color, her skin so pale it caused Khan to gasp quietly. He was instantly on his feet and by her side before John could even open his mouth to protest.

Khan stroked her hair softly and gazed intently at her face. She was breathing slightly under the oxygen mask that covered her mouth and nose. Her skin was icy to his touch when he ran his fingers over her still cheek. He pulled his hand back when he realized he was shaking, and turned to John, his jaw clenched.

“Irene?” he asked, fury emanating from his frame. The Woman had made a bad choice when she’d gone after Molly Hooper. John answer surprised him into immobility though.

“No,” the doctor said, shaking his head as he gave a bitter laugh. “You.”

The look that he gave Khan stunned him even more than the response to his question. It was practically venomous, as John brushed past him to pull the covers closer to Molly’s still form.

“I convinced her to forgive you,” he said, angrily. His words cut Khan into pieces as he listened. “I convinced her to go to your room and see you. She got there after Irene had left and found you on the floor. She contacted Lestrade and myself, explaining the situation and telling him to go after Khan while I needed to get to your quarters. When I made it there, she was,” his voice broke, “she was performing CPR, keeping you alive.”

He ran a hand over his face, obviously trying not to tear up as he refused to meet Khan’s eyes.

“She knew that you’d been poisoned, knew how it had happened, knew that it would have been an incredible dosage, but she didn’t even think about herself. All she thought about was you.”

He finally looked up at Khan, misery and anger mingled in his face.

“And it might kill her.”

Khan stood perfectly still for a moment, looking down at the still woman who held his heart. Guilt and fury fought for dominance in his mind. He crossed the room to get a syringe and rolled his sleeve up, intent on taking his blood and giving her some of it to aid her healing, but John voice stopped him.

“Lestrade already did it. He was here within minutes of hearing that Molly was down.”

\-----------------------------------

Khan’s quarters were destroyed when John let himself in several hours later.

After realizing that he was useless, Khan had nodded once and left the medical bay. Lestrade came by to check on Molly about an hour later, shaking his head.

“He swept onto the bridge like a bloody tornado,” he said wearily. “At least Wiggins had managed to save a lot of the original data before that witch switched it on us, or I think he’d have torn the ship apart with his bare hands to sate his fury.”

With Lestrade’s words in mind, John had left him to watch over Molly, who showed no real progress, and went in search of Khan.

Entering his quarters, he saw that the silver-headed man hadn’t been exaggerating. Khan sat in the midst of the destroyed room, his hair mussed, face pale, feet bare and bloody as the remains of his furniture and other possessions lay in pieces around him. There was broken glass all across the floor and John had to pick his way across the room. He squatted next to Khan, who had not yet acknowledged the doctor’s presence.

“Khan,” he said, lightly tapping his shoulder. The augment literally collapsed at his touch, crumping into a ball, holding his knees tightly to his chest as tears formed in his eyes.

“It’s my fault,” he murmured, sounding dazed. “It’s all my fault. I was stupid, foolish, and the only one who gets hurt is her. It’s always her.”

John sat delicately next to the shaking augment and put a hand on his shoulder, offering silent comfort as Khan fell apart.

\----------------------------

Molly’s eyes fluttered open and she was struck by a sense of déjà vu as she slowly looked around. She was in her own bed in her quarters, and a vase of cheery flowers sat on her bedside table. This time though, they were gorgeous red roses, and as she gingerly sat up, she saw that her entire room was filled with flowers of varying colors and types, and in the middle of it all sat Khan in an armchair she’d never seen before, fast asleep.

**Notes for the Chapter:**

> Cool readers leave a review. Just sayin' ;)


	15. Recovery

**Notes for the Chapter:**

> Hey hey hey, an update! A small one, but an update none the less. The next chapter will have a lot of action and introduce at least one new character. I'll let you guess who that will be haha Enjoy!

The second he opened his eyes, he felt the air figuratively go frigid. Molly was out of bed, and had covered him with a blanket. It was the movement of her tiny hands tucking the warm material around him that woke him. When he stirred, she froze. He cast his eyes upwards and saw her retreat into herself, pulling her hands back quickly and taking a step back, away from him.

He reached towards her, but she stepped back again, shaking her head. He dropped his hand to his lap and stared down at it. Anything to keep from seeing the hurt and reproach in Molly’s eyes. He knew he had betrayed her trust, even though they had not been in a relationship. He cursed inwardly, knowing that it would be ten times harder now to convince her that he truly wanted to be with her.

“Please leave.”

Molly’s voice was quiet but clear, cutting through the thickness of tension like a knife. Khan tensed.

“Molly, I-” he began, trying to explain, trying to make her understand.

“No. Just go,” she sighed, pointing to the door. He stood slowly and walked to the door, pausing to look back at her as she followed him, prepared to lock it behind him. He leaned back into the room, holding himself up with a hand on each side of the door frame. Before she could dart out of reach, he kissed her tenderly on the cheek.

“Thank you, Molly Hooper,” he said sincerely. “I’m glad you are all right.”

He turned and left, missing the sight of Molly pressing her hand to her cheek as if she’d been slapped, tears pooling in her eyes.

\-------------------------------

“How long was I out?”

Molly sat on her bed facing John, who sat next to her, with Wiggins in a chair next to the bed. Both men had come to see her; the doctor to check her vitals and overall well-being, and the hacker because he’d taken quite a shine to her, and though he wouldn’t admit it, had been distraught at the thought of ‘the missus’ not making it through her ordeal.

“Not quite two days,” John answered, taking her pulse at the same time. “We were worried you wouldn’t pull through. Lestrade gave you some blood right away, but Khan kept giving it to you every few hours while you were unconscious. It’s a bloody miracle you made it Molly.”

“I know,” the petite woman sighed, reaching out to grasp the doctor’s hand and squeeze. “Thank you for taking such good care of me.”

“Well you’re welcome, Molly, but you know it wasn’t me.” John paused, seeming to search for words. “Are you, can you, ever forgive him you think?”

The pathologist let out a short, hoarse bark of laughter, while shaking her head.

“I don’t know, John. I was set to forgive him, accept him. Now,” she broke off, looking away uncomfortably.

“Look Mols, I know that he messed up. And he knows it too,” John shook his own head. “God, does he ever know that. But he really does love you. You should have seen him.”

“You should see his quarters,” Wiggins piped up. “Bloody well tore them apart he did.”

Molly glanced at him, surprised.

“Why would he do that?” she asked the scruffy man. Wiggins shrugged.

“Dunno. Impotence maybe? Khan might look like nothing fazes him but he’s got more emotions than a pregnant lady,” he quipped, making Molly and John both chuckle softly.

“I suppose you are right there,” John agreed, closing his medical kit. “He tries to be cold and detached, and I suppose to most people, it appears that he actually is. But when he, feels, for someone,” he paused, his brow furrowing as he gazed at Molly appraisingly. “Well Molly, when he feels for someone, he’d take on every single Klingon in existence if he had to, just to keep them safe. To keep you safe.”

Wiggins nodded sagely.

“He’s right missus,” he chimed in. “The boss don’t love much but when he does, I pity the one who takes it from him.” He smiled ruefully. “I wouldn’t want to be that Irene woman when he catches up with her. He’ll take her apart piece by piece for harming you. Whether she meant to or not.”

Molly frowned, thinking over Wiggins’ words.

“He’s not,” she stopped and started over. “He isn’t actually looking for her, is he?”

Wiggins and Watson shifted uncomfortably, giving Molly all the answer she needed.

“I see,” she said thoughtfully. John motioned to Wiggins that it was time to take their leave.

“You look fine now Molly. Just try to get some more rest. We’ll uh,” he paused. “We’ll try to keep him out of here for now, yeah?”

Molly nodded her thanks as both men exited her quarters, leaving her alone with her thoughts.

\--------------------------

“We’re going down there and that’s final.”

Lestrade groaned audibly as Khan snarled out the order.

“Khan, no offense, but we haven’t had anything good in over a week. Not since that she devil wreaked havoc up there, and just because you’ve got a hunch doesn’t mean we should expose ourselves.”

Khan’s brow raised as his lips curled into a cruel sneer. He was angry, had been since the incident and Molly’s subsequent rejection of him, and it was bleeding over in to his interactions with the crew.

“A hunch from me is better than any evidence you could come up with on your own,” he sneered. “We’re going down there, everyone. Only Wiggins will stay up here to protect my,” he caught himself, “to watch over Molly.”

“I’ll do my own protecting thank you,” came a clear voice from behind him, and Khan froze.

Molly had pointedly avoided any interaction with the commander in the rare instances that she left her quarters. He cursed silently at whoever had informed her that there would be a meeting concerning his plans to go back to Earth and pursue a lead on more information.

“Doctor Hooper,” he greeted her with a nod as she stalked past him to the table. Lestrade stood quickly and offered her his chair, which Molly took with a grateful smile at the silver-haired man. Khan’s jaw clenched.

“As I was saying,” he began again, his tone icy as he gazed at the members of his small crew. “We will go down at 1600 and be back before 00 if we are lucky. In, out, back to the ship, got it?”

Molly nodded and Khan tensed, knowing he would have to fight to keep her aboard the _Vengeance_.

“Doctor Hooper, you will not be in the landing party,” he ordered, watching as her eyes narrowed at him.

“Oh? And why is that? You’ll need every one of us down there and you know it. It’s stupid to leave me up here and have to leave someone with me. That’s puts you two men down,” she retorted, leaning forward in her chair.

“You’re a liability and we could all focus better if you weren’t in the line of fire,” he snapped back.

**_I_ ** _will focus better if I know you are safe._

“I’m perfectly capable of handling myself,” she said stubbornly.

“Oh? As I recall, you foolishly almost got yourself killed only a few days ago. I don’t believe that qualifies as handling yourself well,” he challenged.

“I saved your bloody arse,” Molly spit right back, not backing down. “Now, I’m going and that’s it.”

Khan stared at her for a moment, before hunching his back and running a weary hand through his hair.

“Fine,” he said curtly, making a mental note to speak to Lestrade and Donovan in private about keeping a close watch on Molly while on the surface.

**Notes for the Chapter:**

> Come talk to me on Tumblr. My url is liathwen-slays-dragons. Because I am awesome.


	16. Ambush

**Notes for the Chapter:**

> Huge thanks to mizjoely and ondayer for looking over this for me! Onedayer's trekcheck is a lifesaver I swear!

“Sad day when it’s too quiet for my tastes,” Watson joked lamely as he and Molly stood in the middle of a deserted warehouse. He gestured around at Khan and the others who were investigating around the large area. “It’s just,” he tried to explain, but Molly cut him off with a nod as she gazed warily up at the decaying floor above them. The building was old and unused for years, and the upper floor and some of the roof had rusted away, exposing chunks of blue sky through the metal of the ceiling.

“I know,” she said quietly. “Nothing is ever calm around him. Being with him is like being in the middle of a storm at all times. The world doesn’t seem right without the roaring of the wind in your ears.”

John stared at her for a moment before whistling between his teeth. “Christ Molly, that was really deep,” he said, chuckling slightly. She merely shrugged and kept looking up.

“So?” he asked after a beat. “You gonna forgive him?”

Molly sighed and finally looked at the doctor. “I already have honestly. We were both foolish. I can’t deny him, not when I feel just as strongly as he does.”

John smiled. “I’m glad to hear it. You’re good for him. And God knows, he needs someone to even out that temper of his.”

Molly smiled back at him fondly. “I don’t know about that, but I’m tired of denying my feelings.” She shrugged again and gestured idly around. “I’m in love with him. Why torture us both when accepting him is potentially so much better? I’m not going to tell him just yet though,” she added as an afterthought. “Not until the time is right.”

John nodded, and they fell silent, watching the others poking around the old place. Wiggins had been digging through the Starfleet database and had stumbled upon the coordinates for the warehouse tucked away on the outskirts of London linked in with some files about the augment program. Khan had latched onto it, and decided that an investigation was fully necessary so there they were. The only members of the crew who had stayed behind onboard the _Vengeance_ was Wiggins and the older woman, who had introduced herself as Mrs. Hudson. She was having trouble adjusting to the ship and so spent many hours in her room, bemoaning the loss of her ‘herbal soothers.’

A frustrated roar sounded from Khan’s direction and Molly and John exchanged looks as the augment strode towards them.

“NOTHING!” he yelled. “Nothing!” He kicked at a rock, sending it flying. “There’s nothing here,” he growled as he reached them. “We came for no reason.”

“Well we knew it was a long shot when we decided to come,” John said, and Molly nodded in agreement.

“There’s got to be something though,” Khan bit out, frustrated. “The records can’t just vanish, not all of them. SOMEONE has to know what happened to us, how this all began!”

He scooped up another rock and threw it into the metal wall a good 20 feet from them, managing to dent it. Molly flinched at the loud sound and took a step away from the angry man. He softened, looking a bit ashamed as he noted her reaction. He turned away to call to the others.

“All right!” Khan yelled, his voice echoing in the old building. “Let’s get back to the ship, there’s nothing to find here.”

Molly turned to walk towards the door, smiling at Lestrade and Donovan who trotted up, covered in dust.

“You ok?” she asked them, to which they both nodded, wiping at their grime covered faces. Molly glanced back at Khan, who was standing alone in the middle of the warehouse looking around one last time, impotent rage written on his face.

\---------------------                                                                                                       

Molly regretted wishing for the storm.

One moment, there was silence in the warehouse, the next a shot rang out and Khan roared in agony, clutching his chest, just above his heart. Molly scrambled to roll over as Donovan picked herself up, having knocked Molly to the ground in an attempt to protect her. The woman gave her a grim smile and in the next breath, she and Lestrade were off, scaling the ladder to the second floor. John was at Khan’s side, examining his wound, while simultaneously attempting to hold the furious augment down as Khan tried to get up and protect Molly.

“Molly!” John shouted over the clamor. “Get over here before he kills me to get to you!”

Molly scurried across the warehouse, heedless of her own safety, and crashed to the ground next to Khan, her hands on his torso. She quickly straddled his hips, covering the lower portion of his body with her own and took his face in her hands, forcing him to look at her.

“I’m fine, I’m fine!” she almost screamed. “Let John look at you!”

Khan grunted, still attempting to rise, but careful not to hurt the woman on top of him.

“I’ll be all right,” he finally growled, pushing himself up with his good arm to sit with Molly still on his lap. “Augment, remember? And it didn’t hit my heart. Lousy assassin, that one,” he muttered, his brow furrowed in thought.

“Khan, why is this a wound from 20th century weapon? No one uses those anymore, it’s all phasers now,” John whispered, worriedly. Molly watched Khan’s jaw clench as blood poured from his wound.

“I don’t know,” he said through clenched teeth. “I bet it has something to do with us though,” he added, shifting Molly to the ground, but keeping a firm arm around her, refusing to let her leave his side. His electric blue eyes scanned the upper floor where the sounds of running were occurring. Seconds later there was silence and all eyes turned upwards.

“Got her!” Lestrade’s voice rang out from the second floor, accompanied by the sounds of a scuffle.

He appeared moments later followed closely by Donovan, both of them holding onto a small blonde woman who was struggling in vain. They pulled her down to the first floor and over to Khan, Lestrade cursing as she managed to sink her teeth into him.

Molly hovered protectively over Khan as Sally threw the 20th century era sniper rifle she held in one hand to the floor next to Khan.

“That’s it,” she said tersely, her other hand still clenched around the sniper’s upper arm. Molly examined the woman carefully, aware of an idea, just out of reach, in the back of her mind. The woman was small, as short as Molly, and just as delicately built, though her slim frame boasted more muscle than Molly’s did. Her blonde hair was cropped short around her head, reaching only her chin, and her piercing blue eyes shone out from her pale face, fixed firmly on Khan.

Khan rolled over and got to his feet slowly, his opposite hand putting pressure on his wound. He leaned forward, invading the woman’s personal space in an act of intimidation.

“You missed,” he said cruelly. “And now, do you know what I’m going to do to you?”

Molly held her breath as the woman stared back at Khan silently, her small frame unwavering in the face of his overwhelming presence, thin lips set in a grim line. The woman’s eyes darted towards her for a second, and Molly’s brow furrowed at the expression there. Molly could almost swear that it was pity.

Khan reached down with a grunt of pain and closed his bloody hand around the gun.

“I’m going to kill you,” he said simply, hefting the weapon easily. Molly’s eyes widened and she instinctively threw an arm out to grasp Khan’s sleeve. The woman’s gaze shifted to John’s and Molly was surprised to see her lips part a bit as she stared at the doctor silently.

“No!” she shouted, pulling on Khan desperately. “No you can’t do that!”

He turned his head to the side, giving her an incredulous glare.

“She just attempted to assassinate me Molly, she deserves death.”

“No she doesn’t! Take her back to the ship, put her in the brig. Maybe you can get her to talk, just don’t, don’t kill her Khan,” Molly ended in almost a whimper, tears forming in her eyes. “Don’t kill her.”

He stared at her for a long moment before grinding his teeth together. “No! You won’t sway me in this Molly. You were wrong about Irene and it nearly cost us dearly. I won’t have you in danger again. She deserves this, she deserves to die.”

He walked away from the group, as Lestrade and Donovan looked at each other over the woman’s head. Molly glanced helplessly at John, whose eyes were fixed on the assassin, with a look that Molly couldn’t quite place. Khan turned to face them and raised the gun up as Lestrade and Donovan forced the woman to her knees. John looked up and met Molly’s eyes, tears forming in his own and Molly couldn’t stop herself from crying out.

“Khan no! I’ll accept you! I’ll be yours, just please please don’t kill her. Take her back to the ship, unharmed, and I’ll do whatever you ask of me.” Molly ran to him, pulling the gun down as everyone stared at her, stunned.

The woman on the ground lifted her head, once again fixing her eyes on Molly’s, and nodded slightly, a gesture of gratitude. Khan dropped the gun to the floor and stared down at Molly in disbelief.

“You’d give in, just to save this woman you don’t know?” he asked, incredulously. Molly nodded firmly.

“I would.”

Khan looked at her a moment more before walking past her to grab the woman’s arm and haul her to her feet.

“This is your lucky day apparently. Be thankful that I have a soft spot for her, or you would be dead by now.” He shoved her back to the ground and Molly ran to her side, pulling her to her knees. She peered into the woman’s face and smiled tentatively.

“What is your name?” she asked as the woman met her gaze. The blonde blinked once, cocking her head to the side as if thinking, before she replied, her voice sounding hoarse as if it had been a long time since she’d spoken.

“Mary. My name is Mary.”


	17. Interrogation

**Notes for the Chapter:**

> No beta on this one, though miz-joely did read over it to see if it made since so thanks to her!

“Has she spoken yet?” Khan winced as Molly prodded his upper chest, feeling around his wound to ensure that it wasn’t developing scar tissue as it healed rapidly. Lestrade stood behind her, having come to report on the status of the prisoner.

“No, she hasn’t but uh, well there is something going on.”

Khan frowned. “Well spit it out, what is it?”

Lestrade ran a hand through his silver hair and scowled, glancing at Molly quickly. “Well it’s John. He’s, he’s in there with her and they’re just staring at each other, have been ever since we put her in there. Haven’t said a word though, neither of them.”

Khan’s brow furrowed in thought but Molly grinned happily. “See! I knew it wasn’t right to kill her.”

“That remains to be seen.” Khan’s voice was icy as he replied to the small woman next to him. “And don’t think that we aren’t going to be discussing your tactic for getting me to spare her life. She still attempted to kill me, you know.”

Molly flushed, remembering what she had so rashly promised in exchange for the petite blonde to be taken prisoner. It was time though, time for her to accept that Khan really did care for and want her, no matter what happened when or if she could ever help him remember being Sherlock Holmes.

\--------------------

“Mary, why did you try to kill Khan?”

Molly sat in the cell with the prisoner, as well as Watson, who adamantly refused to be removed from the woman’s side. Khan and Lestrade observed the interaction from the other side of the clear wall of the cell, ready to step in if needed. One glance in Molly’s direction was all that John gave when she entered, but Molly saw a new recognition in his gaze, and realized that John had at least some memory of the woman.

She felt an intense relief as someone she trusted could remember things. Even with the reassurances of Mycroft, she had questioned herself more than once, wondering if she was making it all up, all of their shared past. As the days wore on, she noticed new mannerisms, old quirks in each of her companions and could now remember at least a bit about each person. John was first, the realization of his former self nearly bowling her over as she walked into the Sick Bay one day. Donovan had taken her the longest, but now that she could place the woman as being under Lestrade in New Scotland Yard, she assumed it was because Molly herself had had limited with the other woman. The others had come slowly to her, and she couldn’t remember everything about each person, just vague bits.

Their captive though, was a mystery to her, and before John had so obviously recognized her, Molly had wondered whether she had been a part of their past, or a product of this new age. Molly turned her attention back to the prisoner, breathing out slowly.

The blonde woman stared at Molly, her expression frosty. “I was told to wait for you. He knew you were coming. But,” she paused and frowned, her gaze dropping to the floor. “I didn’t follow orders.”

Molly’s brow furrowed in confusion. “You mean you missed and didn’t actually kill him?”

The prisoner suddenly became very interested in her hands, which were clasped in her lap. “Well no. I didn’t mean to kill him actually. I knew he was an augment, and that I’d have to be precise if I wanted to end his life. I just shot close enough that it would seem like a mistake if anyone cared to look. But that’s not what I meant when I said I didn’t follow orders. I, well I was told to kill you actually.”

Khan’s fist collided with the clear barrier, making Molly jump and yelp in fright. He was scowling, and looked as if he was about to enter the cell, but Molly held up a shaky hand to him and turned back to Mary.

“Do you, do you know why? Or who it is that wants me dead?”

Mary shook her head. “I don’t know why. I’m an assassin, I kill who they tell me to kill. But I assume it’s because he cares about you.” She turned to stare at the augment outside the cell. “It would hurt him worse if something happened to you, than if it happened to him,” she said, still watching Khan. After a moment he, unbelievably, nodded curtly at her, looking at her with an expression that Molly tentatively called respect.

“Well then why did you shoot Khan instead of me?” Molly asked, leaning forward.

Mary glanced back at her, looked down at her hands. She then held them up to show Molly. “I can’t remember much about before I woke up. But I do know, I might have killed people, but I didn’t kill innocent people. I’m not bad, I’m not. I know I’m not. And while I was watching you all, I could see that you were innocent and good. But him,” she jerked her head in Khan’s direction. “He’s killed a lot of innocent people. If I had to kill someone, I would at least kill someone who deserved it. I changed my mind at the last moment though. I think it was the look he gave you. He’s capable of caring, I just didn’t see it until then.”

There was total silence following her speech. Finally, Molly swallowed thickly and turned to look at Khan, who was perfectly still, his face stricken, almost guilty. He caught Molly’s gaze and turned abruptly, leaving the three in the cell, and Lestrade outside of it.

“Molly,” John whispered, leaning forward so that Lestrade wouldn’t see him speaking. “I remember things. She triggered it. I remember.”

Molly nodded slightly, and stood. “I’ll speak to you later,” she murmured to John, and leaned down to take Mary’s cold hand in hers, surprising the blonde. “If it makes any difference,” she said earnestly, “I don’t think that you are bad either.”

She turned to go, but Mary’s voice stopped her.

“Moriarty. His name is Moriarty.”

Molly nodded, her back still to the couple in the cell, and motioned for Lestrade to let her out.

\----------------------

The door clicked closed behind Molly, as she stepped in Khan’s quarters for the first time since she’d nearly died saving his life after Irene poisoned him. She shuffled nervously, looking around for the augment. His voice sounded from the other side of the great bed.

“She’s right, you know. I’ve done a lot of bad things. Too many.”

Molly crossed the room quickly and found him seated on the floor, his back against the bed. She seated herself next to him and sighed.

“Yes.” She agreed with him, nodding. “Yes you have done a lot of bad things.” She angled her body towards his and picked up one of his massive hands in both of hers. “But those things, they don’t have to define you. I know that deep down, you are good too. Even the best people make bad choices sometimes. You didn’t know what else to do.”

He sighed and pulled her hands up, pressing a light kiss to the back of each.

“I will ruin you Molly. I’m a danger to all who know me. You should be running.”

She smiled, remembering all the times when he was still Sherlock that he’d torn her apart with careless words, knowing that she’d never run before, and that she never would.

“I’m not afraid of you,” she whispered, getting up onto her knees next to him to better see his expressions. Khan stared at her before cautiously lifting a hand to touch her face. He trailed a single finger down her cheek to her throat and then around to sink his hand into her hair and pull her towards him slowly. He gave her time to pull away but she didn’t, instead sighing and leaning into his warmth. His full lips found hers, parting them to give her passionate kiss.

The first since her promise to give herself to him in exchange for Mary’s life.


	18. A Crack in the Ice

**Notes for the Chapter:**

> *sheepishly waves hello*
> 
> Hi... long time no see. Sorry about that. Life happened. I love you all, please don't be upset with me.

Khan sighed into Molly’s mouth, his lips slotting across hers like they belonged there. Her taste was intoxicating, drugging him, both dulling and heightening his awareness at once. He could feel her pressed against him, her tiny frame wrapping around him as he pulled her into his lap.

Her legs parted and she straddled him, rolling her hips against his, panting softly between feverish kisses. He growled and nipped at her lip making her gasp, taking advantage of her parted lips to dip his tongue into her mouth, tasting her thoroughly as his hands fell to her hips, grinding her down against his growing erection. Her moan threw him into a frenzy and he pushed her off, getting to his feet and immediately grabbing her again.

He pressed her against the wall next to the bed, trapping her there with his body, his hands eagerly roving over every inch of her skin he could find. He slipped his hands under her shirt, reveling in the soft skin of her back, and pulled away for a brief second to divest her of the garment. Molly eagerly allowed him, before pulling him back to her, kissing him as if her life depended on it.

He picked her up easily, pressing her into the wall, as he kissed her. Turning, Khan gently deposited her onto the bed and stood back, looking at her, pulling his own clothes off until he stood in only his pants. Molly swallowed self-consciously.

“I know they’re small…” she began, but Khan growled, cutting her off.

“The only one who has a problem with that is you, Molly. I think…” he reached for her, easily undoing her bra with one hand. “That you are perfect the way you are. No need to compensate for the size of your breasts.”

Molly stared at him, dumbstruck. After a moment, Khan’s brow furrowed.

“What?” he asked, confused by her reaction.

Molly frowned, and shook it off, reaching for him. “Nothing,” she lied, firmly pushing Sherlock’s cruel words from her mind.

Khan’s eyes narrowed but he allowed her to pull him down to rest between her thighs. His eyes closed as he ground himself against her, slowly rolling his hips. Molly moaned, holding him tightly, panting lightly as he moved against her.

He moved back and unbuttoned her trousers, slowly pulling them down her legs. He took his pants off then his hands went back to her and hovered over her knickers. Khan looked up and met Molly’s gaze.

“May I?” he asked. “You don’t have to if you don’t want to. I don’t want you to think I’m forcing this, I just-” he stammered, finally stuttering to a halt.

Molly smiled and took his hands in hers, placing them on either side of her hips.

“You may,” she replied, and Khan grinned eagerly, pulling her knickers off of her quickly. Another second and he was covering her with his body again. He ground his erection into her, making her moan loudly and spread her legs farther. He teased her, grasping his cock to rub the head against her clit which caused her to gasp and bit her lip to keep from uttering curses.

“Oh god, Khan, just do it,” she whined, and he relented. Khan gently pushed into Molly, slowly pressing farther and farther as she writhed and moaned, clutching him closer to her. When he was finally fully inside her, he pushed up and held himself above her, searching her for any sign of pain.

“All right?” he asked, and she nodded. He smiled at her, and brushed a piece of hair from her face. He began a slow pace, one that could only be described as making love. He worshipped Molly’s body, his fingers rubbing lightly on her clit as he moved inside her, until she cried out in ecstasy.

He kept up the gentle pace almost until the end, his hips moving faster as he sought his own release. Molly held him tightly as he came with a whimper, then nuzzled against her. He moved off of Molly, laying next to her and wrapping his arms around her as they lay there.

“Hmmm,” he murmured after a while.

“What?” Molly asked, shifting in his arms to look up at him.

“Somehow I thought I’d be a more forceful lover,” he said, lips pursed as he thought. “I’m forceful in almost every other aspect.”

Molly nodded, wondering if Sherlock was showing through Khan’s personality.

“For some reason, I needed to be gentle with you. I needed to make up for…” he trailed off, and looked at her, puzzled. “I don’t know what I needed to make up for, but I needed to.”

Molly frowned, as Khan’s brow furrowed.

“Don’t think about it now,” she said, snuggling closer to him. “Just rest. Maybe it’ll come to you on it’s own.”

Khan nodded slowly, holding her close. Both were soon fast asleep.

\----------------------------------------

Khan came awake with a roar, sitting bolt upright in bed. Molly yelped, startling awake as well. He shook, and she took his hands to calm him.

“Shh, shh,” she soothed. “It was just a dream. Just a dream.”

“It was so real,” he said, his voice shaking. “It was so real. I was standing on the top of a tall building, looking down. John was down there. I was going to jump from the building. I was going to die, Molly. I don’t know why, but I was going to die.”

Molly swallowed thickly, remembering the day vividly.

“It’s okay, I’ll protect you,” she said, rubbing a hand across his back in a soothing gesture. He looked at her curiously.

“What could you possibly do?” he asked, confused.

Molly shook her head, turning slightly away from him so that he couldn’t see the tears in her eyes.

“Nothing,” she replied. “You could probably say thank you,” she continued, nodding towards her hands which were still rubbing his skin softly.

“Thank you,” he replied slowly, his brow furrowed.

“Come on,” Molly sighed. “Let’s go back to sleep.” She turned, back to Khan, and lay back down. A moment later, he followed suit and they both lay with their thoughts until sleep overcame them once more.


	19. Memory

Khan sat, head in his hands, in the chair that sat in the corner of his chambers. Molly slept peacefully in the bed, limbs sprawled out, taking up every inch of space possible. Khan half-smiled, thankful he had a large bed, otherwise, he might have fallen out of it during the night.

He sobered quickly though, his mind running over and over the dream from hours before. He’d gone back to sleep briefly, but had awoken again after dreaming a second part. He’d dreamed that he was standing on the roof of the building and that he’d watched as John was knocked to the ground. He jumped then, somehow, unafraid, As he fell, he felt a sharp tug behind him and realized that a cord was attached to his coat. He flew backwards through the air and crashed into a window of the building.

And there, standing before him, was Molly.

That was when Khan knew it wasn’t a dream. It was a memory.

You could say thank you…

Khan watched as Molly slept, chest moving with each breath.

He kissed her, passionately. Khan could feel the desire he held for her through the dream. Judging from the surprise in her body language, he’d say that it was the first time he’d kissed her. Then, just as suddenly as it began, the kiss ended and Khan was walking away, off to do something that just barely eluded his faded memories.

He shook his head and stood, stretching, before padding softly into the bathroom. He closed the door behind him and rested his hands on the counter, looking intently into the mirror. His brow furrowed and he reached up slowly with one hand, taking a lock of his hair between his fingers and twisting slightly. It curled easily and he stared at it for a long moment, thinking of Molly’s exclamation of what he’d done to his hair from the first time she’d seen him after waking from the cryosleep.

Hearing Molly stir in the other room, Khan quickly smoothed his hair back and picked up his toothbrush. He began cleaning his teeth, and was joined by Molly after a moment.

“What are you doing awake?” she murmured, hugging him from behind, arms locked around his waist. She was still deliciously naked, while he had been cool enough to warrant a pair of pajama bottoms. She shivered and he frowned, pausing in his efforts.

“Go back to bed,” he muttered around the toothbrush. “I’ll join you in a minute.”

She nodded and silently left the room. Khan finished brushing his teeth a moment later and made his way to the bed, eager to make love to her once again before they greeted the day.

\------------------------------------------------------------------------------

“John, might I speak with you… in private?”

Watson nodded, and Khan led him from the bridge to a secluded room near the brig where Mary was still being held prisoner.

 **"** Tell me what you remember,” Khan demanded, as soon as the door was closed securely. John’s brow furrowed and he looked at Khan curiously.

“Are you starting to remember things too?” he asked.

Khan nodded. “I had a dream last night.” He related the dream to John, who pursed his lips in thought.

“That rings a bell somewhere, but I don’t remember it exactly. I remember Mary mostly. We were… I think we were married. And I remember a baby.”

Khan’s eyes widened. “A baby?” He thought back to putting his family into the tubes and the image of a small child, maybe a year old, flashed into his mind.

“Isabel?” John muttered to himself, shaking his head. “I can’t remember.”

“I saw a child, in the cryotubes. A baby.” Khan shook his head as well. “A little girl. Blonde, pale skin. She could easily be your daughter if what you remember is correct.”

“My… my daughter?” John asked, his voice wavering. He sat, almost in shock, for a long moment.

Khan stood, pacing back and forth. “We need to get her back. We need to get them all back and find out why we were put into cryosleep in the first place.”

John nodded and stood as well. “Khan?” he asked, waiting for the other man to look at him. “Can I… Can I tell Mary?”

Khan thought for a moment. “You don’t think she’ll try anything?”

John shook his head emphatically. “No. She remembers me and some more besides. She recognizes Molly as well… oh that reminds me.” He paused. “Mary said something interesting last night after you and Molly left. She said, ‘she’s the key.’ Weird, huh?”

Khan frowned. “The key to what?”

“I don’t know. I bet if you let Mary out of the brig she’d be more willing to tell you what she knows though,” John said.

Khan sighed. “As long as you keep an eye on her. We don’t want another Irene fiasco on our hands,” he replied.

“Scout’s honor, sir,” John answered, with a grin. “Is that all?”

Khan nodded. “Tell Lestrade I said to let Mary out with the condition that she be shackled to you until I trust her enough to let her wander on her own.”

“Yes, captain,” John replied, and was out the door like a shot.

“The key to what?” Khan said again, this time to empty air. He heaved a heavy sigh and left the room, in search of Molly.

\------------------------------------------------------------------------

Molly sat in the cell with Mary, silently watching the blonde woman.

“Tell me,” she said finally.

Mary looked at her coolly. “Tell you what?”

“Tell me what happened after you woke up,” Molly replied, exasperated.

“There’s not a lot to tell.” Mary examined her nails, not looking up. Molly squatted next to her and maneuvered into her line of vision.

“I remember you, Mary,” she said. “I remember exactly who you are. For them to have placed you where you were, they had to have known as well. Please, tell me everything.”

Mary sighed. “Okay. But there’s not much to tell you. I remember waking up and I was cold, so cold. And my heart ached. I missed someone but I didn’t remember who or why I missed them. I kept hearing a baby cry. It drove me crazy those first few weeks until they came for me. A short, dark haired man and a burly blond. Moriarty and Moran, they were called. They told me that I’d be ‘plying my trade’ once again. When they handed me a gun, not a phaser, a gun, I knew exactly what they meant.

They had me kill several people. Some politicians, some wealthy people. It didn’t really matter to me.” She stopped for a moment to collect her thoughts. “You couldn’t understand. John does. When I have a gun in my hand and a target before me, everything is quiet. There are no more voices in my head. No more babies crying, no more echoes of something I once had. It’s peaceful. That’s why I did it. To keep my sanity.

Anyway, time passed, I don’t know how long, then they sent me after you. They wanted you eliminated before he starts to remember. They said that you are the key to his memories and without you he’ll never return to his former self. They said without you that he’ll spiral downward and become the thing he hates most.”

“And what is that?” Molly asked.

Mary smiled coldly. “Death.”


End file.
